Linux4Chemistry Open Source Freeware Free for academics Shareware Commercial [Explain] All categories 2D Draw 3D Viewer Cheminformatics Crystallography Docking Education Electrochemistry Mass Spectrometry Molecular Dynamics Molecular Mechanics NMR Quantum Mechanics Reactions Thermodynamics Other categories

Chemistry Section of the WWW Virtual Library

Linux4Chemistry is maintained by Noel O'Boyle. Original maintainer (2001-2005) is Nikodem Kuznik. To add a program or leave a comment, click here. Keep informed of new entries with our RSS feed. Keep up to date with the CCL list with this unofficial RSS feed.

• 2D   Quantum Mechanics

  GPL, Fortran

  • 2D is a numerical Hartree-Fock program for diatomic molecules.

• ABINIT   Quantum Mechanics

  GPL, Fortran

  • ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation).

• ADF   Quantum Mechanics

  • ADF is the Amsterdam Density Functional program system for high-quality computational chemistry research. The two main programs are ADF, for molecules, and BAND for periodic structures: polymers, slabs, and crystals. Several smaller utility and property programs are available for pre- and post-processing data of the main calculations.

• Almond   Cheminformatics

  • ALMOND is a program specifically developed for generating and handling alignment independent descriptors called GRIND (GRid INdependent Descriptors). These are a new generation of 3D-molecular descriptors with application in 3D-QSAR, QSAR, virtual screening, design of combinatorial libraries, selectivity studies and in any field where 3D quantitative pharmacophoric description for (macro)molecules is needed.

• ALOGPS   Cheminformatics

  • ALOGPS provides prediction of logP and aqueous solubility of compounds to be used in drug design (ADMET and HTS) and environmental chemistry studies. The ALOGPS program can be also used to predict logD values.

• AmberFFC   Molecular Dynamics

  • AmberFFC is designed to convert the different existing AMBER force fields (FF) freely available in the public domain, for use with commercial molecular modeling packages, using the MSI software package as a case model.

• AMMP   Molecular Dynamics, Molecular Mechanics

  GPL, C

  • AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms.

• AMPAC with GUI   Quantum Mechanics

  • AMPAC is a fully-featured semiempirical QM program. It also includes a graphical user interface (GUI) that builds molecules and offers full visualization of results.

• AQUA   NMR

  • AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA is capable of calculating NOE violations, the level of completeness of NOEs based on the structure.

• ASAD   Reactions

  • ASAD is a software package developed for creating and integrating chemistry schemes in atmospheric models without the need to write any FORTRAN code to solve the chemical rate equations.

• Ascalaph Quantum   Quantum Mechanics, Molecular Mechanics, 3D Viewer

  GPL, C++

  • Ascalaph Quantum is a GUI for preparing molecular mechanics calculations. It also provides an interface to PC GAMESS, NWChem and CP2K.

• Atomistix ToolKit   Quantum Mechanics, Nanostructures

  • Atomistix ToolKit, ATK, is a first principles electronic structure program capable of modeling electrical properties of nanostructured systems coupled to semi-infinite electrodes (using non-equilibrium Green's functions). The key features are calculation of electrical properties of nanoscale devices, access to advanced DFT algorithms, support for molecular systems, bulk and periodic systems, and two probe systems. In addition there is a Python-based scripting environment.

• AutoAssign   NMR, Enzyme

  • AutoAssign is a constraint-based expert system for automating the analysis of backbone resonance assignments using NMR spectra of small proteins.

• AutoDock   Docking

  GPL, C++

  • AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Search methods include evolutionary methods such as the Lamarckian Genetic Algorithm, in addition to the Monte Carlo simulated annealing (SA) method.

• Avogadro   Quantum Mechanics, Molecular Mechanics, 3D Viewer

  GPL, C++

  • Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering engine and a powerful plugin architecture.

• Babel   Cheminformatics

  • Babel is a program designed to interconvert a number of file formats used in molecular modeling. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.

• BallView   3D Viewer, Molecular Mechanics, Molecular Dynamics

  GPL, C++

  • BallView is a cross-platform molecular visualization tool with support for molecular mechanics optimisation, molecular dynamics and molecular editing. It supports a large number of file formats, SMILES and SMARTS, as well as forcefields such as Amber, MMFF94 and Charmm. Its capabilities also include realtime raytracing and stereoscopic viewing. Actions can be automated using Python scripts.

• B-BOP   Quantum Mechanics, Molecular Dynamics, Materials

  GPL, C

  • B-BOP (Block Bond-Order Potential method) is a program for performing O(N) tight-binding (TB) calculations of molecules and bulks, based on block bond-order potential method within semi-empirical TB models. Molecular dynamics (MD) simulations for the NEV ensemble and the geometry optimization by the steepest decent (SD) method can be performed.

• BIGMAC   Thermodynamics

  GPL, Fortran

  • BIGMAC stands for Beyond Impressive Goals of Mechanical Artificial Computations. It uses Configurational Bias Monte Carlo (CBMC) to compute thermodynamic properties of flexible molecules. It has been used to study the adsorption behavior of linear and branched alkanes in zeolites and the vapour-liquid equilibrium of linear and branched alkanes.

• Bioclipse   Cheminformatics

  Eclipse Public License, Java

  • Bioclipse is a Java-based visual platform for chemo- and bioinformatics with a plugin architecture that currently includes plugins for the CDK and Jmol.

• Bist   2D Draw

  GPL, C++

  • Bist (Bidimensional Structures) is a chemical drawing program focussed on organic chemistry. Using the OpenBabel API, it can import/export in a wide variety of file formats including CML. A notable feature is that it can automatically parse linear fragments to create a 2D structure.

• BKChem   2D Draw

  GPL, Python

  • BKChem is a chemical drawing program written in Python. One of its notable features is SVG export.

• BobScript   3D Viewer

  • BobScript is a program to facilitate the production of publication quality molecular graphics. It is a further development of the program MolScript, but has extensions that make it particularly suited to protein crystallography. Output can be in PostScript format or as a file suitable for rendering with Raster3D. A conversion program also enables POV-Ray to be used as the rendering engine.

• Bodil   3D Viewer

  • Bodil is a modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing.

• BOSS   Molecular Mechanics, Quantum Mechanics

  • BOSS (Biochemical and Organic Simulation System) is a general purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics (QM) calculations.

• CACTVS   Workflow

  • CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type. CACTVS Tools is a visualization package for chemist.

• CAMEO   Reactions

  • CAMEO is a modular expert system, a computer program that predicts the products of organic reactions given starting materials, reagents and conditions. Online demo - WebCAMEO available.

• Cantera   Reactions, Thermodynamics

  BSD, (Python, C++)

  • Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. You can use Cantera from Python or Matlab to handle problems in areas such as combustion, flame structure, detonations, electrochemical energy conversion, fuel cells, aqueous electrolytes, plasmas and thin-film deposition.

• CASTEP   Quantum Mechanics

  • A fully-featured first principles electronic structure code based on density functional theory and using a plane-wave basis set with pseudopotentials. It uses periodic boundary conditions and is therefore highly suited to modelling solids, liquids, and surfaces using slab geometry. Available for free to UK academics.

• cclib   Quantum Mechanics

  GPL, Python

  • cclib (computational chemistry library) allows users to easily implement computational chemistry algorithms that use the results from calculations from any of a large number of popular computational chemistry packages (incl. GAMESS, GAMESS-UK, Jaguar, Gaussian, Molpro and ADF).

• CCP1GUI   Quantum Mechanics, 3D Viewer

  GPL, Python

  • CCP1GUI is a free, extensible Graphical User Interface (GUI) developed for GAMESS-UK, but also supporting other packages. The GUI has been built around the Python open-source programming language and the VTK visualisation toolkit. It has support for conventional formats such as Z-matrix and PDB, as well as programme-specific formats for CHARMM, ChemShell, XMol and Gaussian.

• CDA   Quantum Mechanics

  • CDA (Charge Decompositional Analysis) has been devised to analyze chemical systems which can be described as donor-acceptor complexes. The electronic and energetic changes associated with the formation of a complex consisting of two fragments A and B are partitioned in terms of the familiar Dewar-Chatt-Duncanson model. The energy analysis is feasible within the Hartree-Fock approximation, while the charge decomposition analysis can also be carried out at correlated levels. Requires Gaussian output files.

• ChemApp   Thermodynamics

  • ChemApp provides the powerful calculation capabilities of ChemSage in the form of a programmer's library. It consists of a rich set of subroutines which provides all the necessary tools for the calculation of complex multicomponent, multiphase chemical equilibria and the determination of the associated energy balances. ChemApp light is the free version of ChemApp, giving you almost the same functionality as the regular version of ChemApp.

• ChemCalc   Utility

  • ChemCalc is intended to be a calculator oriented towards chemistry. It calculates the molecular formula, molecular mass, exact mass, elemental analysis and plots the isotopic distribution graph.

• ChemDoodle   2D Draw

  • ChemDoodle is an innovative 2D chemical drawing application which works on any operating system with Java installed. It contains an abbreviation library which can be extended, and can import and export many file formats including ChemDraw Exchange Format.

• ChemicalInventory   Inventory

  GPL, Java

  • ChemicalInventory is a web application that manages the chemical stock in a laboratory or production facility, where chemicals must be safely stored, easily found and tracked.

• Chemistry 4-D Draw for Java   2D Draw

  • Chemistry 4-D Draw is an easy-to-use and powerful structure drawing program implemented in 100% Java. Users will be able to use the same graphical interface regardless of the types of machines they are using.

• Chemistry Development Kit (CDK)   Cheminformatics

  GPL, Java

  • The Chemistry Development Kit (CDK) are Java utility classes for chemoinformatics and computational chemistry. These classes include descriptor calculation, 2D structure layout, graph algorithms, and chemical file format readers among others.

• CHEMKIN   Reactions

  • CHEMKIN is a set of software tools for solving complex chemical kinetics problems. It allows users to predict the chemical conditions of their system based on variable reactor parameters, inlet gas, and catalyst compositions when applicable. CHEMKIN consists of gas and surface-phase chemical kinetic solvers, and a variety of reactor models that can be used to represent the different systems you are interested in modeling.

• ChemNomParse   Cheminformatics

  LPGL, Java

  • ChemNomParse is a chemical nomenclature parser. The project aims to build molecules from an IUPAC chemical name.

• ChemSol   Solvation

  • ChemSol calculates solvation energies using the Langevin Dipoles (LD) model of the solvent and ab initio calculations.

• Chemsuite   2D Draw, IR, Utility

  GPL, C++

  • Chemsuite is composed of several programs that work independently of each other: Chem2D - a 2D molecular drawer; Molcalc - a molecular weight calculator; chemIR: an infrared spectra processor which can read, process, export and print Perkin Elmer spectra.

• Chemtool   2D Draw

  GPL, C

  • Chemtool is a program for drawing organic molecules easily and store them as an X-Bitmap, Postscript and XFig file. It runs under X- Window and is written with GTK+.

• Chimera   3D Viewer, Molecular Dynamics, Docking

  • Chimera is an extensible molecular modeling system that can be used for molecular visualisation, addition of hydrogens, volumetric data, displaying the results of MD simulations, viewing the output of DOCK, and it has support for writing extensions in the Python scripting language.

• CHIMP   Reactions

  GPL, C++

  • CHIMP (CHIMP Hierarchical Modeling Program) is a generic tool for the modeling of chemical phenomena. CHIMP has the ability to perform dynamic Monte Carlo simulations on chemical reactions, in particular heterogeneous catalytic reactions.

• Cn3D   3D Viewer

  • Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. It can also function as a helper application for web browsers and allows the web browser to show 3-dimensional structures from NCBI's Entrez retrieval service.

• CNS   Crystallography, NMR

  • CNS (Crystallography & NMR System) is a software suite designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.

• COLUMBUS   Quantum Mechanics

  • COLUMBUS is a collection of programs for high-level ab initio molecular electronic structure calculations. The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules.

• Computational Crystallography Toolbox   Crystallography

  GPL, (C++,Python)

  • The Computational Crystallography Toolbox (cctbx) is a collection of fundamental procedures for Computational Crystallography. It includes a unit cell toolbox , a space group toolbox and an element toolbox for the handling of scattering factors and other element properties.

• ConQuest   Crystallography

  • ConQuest is the primary program for searching and retrieving information from the Cambridge Structural Database (CSD). ConQuest provides a full range of text/numeric database search options, in addition to more complex search functionality including chemical substructure searching, geometrical searching, and intermolecular and non-bonded contact searching.

• CONSCRIPT   Crystallography

  • CONSCRIPT generates Gouraud shaded isosurfaces of protein electron density for high quality presentation in journals.

• CORINA   Cheminformatics

  • CORINA (COoRdINAtes), is a rule and data based system, that automatically generates three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table or linear code. CORINA offers many features to influence the 3D generation process, e.g. addition of lacking or implicitly given hydrogen atoms, neutralization of formal charges, orientation of the 3D structures according to their moments of inertia, removement of counter ions in salts.

• COSMOtherm   Cheminformatics, Thermodynamics

  • COSMOtherm provides realistic solvation thermodynamics based on quantum chemical calculations.

• CP2K   Quantum Mechanics, Molecular Dynamics

  GPL, Fortran

  • CP2K can perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. Density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

• CPMD   Quantum Mechanics, Molecular Dynamics

  • The CPMD code is a parallelised plane wave/pseudopotential implementation of density functional theory, particularly designed for ab-initio (Carr-Parrinello) molecular dynamics.

• CP-Optimizer   Quantum Mechanics

  • CP-Optimizer (Counterpoise Optimizer) is an automatic procedure to perform geometry optimisation and harmonic frequency calculations using GAUSSIAN.

• Crunch   Crystallography

  • Crunch is a direct methods program for solving the phase problem in crystallography. Instead of using the usual triplet relation to determine the phases, Karle Hauptman matrices are used.

• CRYSTAL   Quantum Mechanics

  • CRYSTAL computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. CRYSTAL may be used to perform studies of the physical, electronic and magnetic structure of molecules, polymers, surfaces and crystalline solids.

• Dalton   Quantum Mechanics

  • The Dalton Quantum Chemistry Program represents a powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2 or MCSCF wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces, both for static and dynamical investigations.

• Debyer   Crystallography

  GPL, C

  • Debyer takes a file with atom positions as input, and outputs X-ray and neutron diffraction patterns, the total scattering structure function, the pair distribution function (PDF), and related functions such as the RDF (reduced PDF). It can be used for comparison of molecular dynamics simulations or other models of atomistic structure of the material with X-ray and neutron powder diffraction experiments.

• DelPhi   Solvation

  • DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. It is fast, accurate, and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and for treating systems containing mixed salt solutions.

• deMon2K   Quantum Mechanics

  • deMon2K allows the user to perform ab-initio DFT calculations of large systems including transition metals with precision in a relatively short time.

• DENEB   3D Viewer, Quantum Mechanics

  • DENEB is a powerful graphical user interface to many DFT calculation packages as SIESTA, VASP and QE. It is capable of managing hundreds of projects, each containing hundreds of simulations applied to different samples, every one containing thousands of atoms.

• DINO   3D Viewer

  • DINO is a realtime 3D visualization program for structural biology data. DINO aims to visualize all this structural data in a single program and to allow the user to explore relationships between the data.

• Dirac   Quantum Mechanics

  • Dirac (Direct Iterative Relativistic All-electron Calculations) uses FORTRAN (and a bit of C) code for relativistic molecular calculations based on the Dirac-Coulomb Hamiltonian. It solves the the 4-component DHF equations by the SCF iterative procedure and provides tools for analysis of the converged wave function.

• DIRDIF   Crystallography

  • DIRDIF performs crystal structure determination by Patterson methods and direct methods applied to difference structure factors.

• DisMol   3D Viewer

  BSD Compatible, Java

  • DisMol is a molecular viewer applet written in Java, which allows molecular structures to be viewed on the web.

• DL_MESO   Mesoscopic modeling

  • DL_MESO is a general purpose mesoscopic simulation package developed at Daresbury Laboratory as part of a collaborative computational project for the Computer Simulation of Condensed Phases (CCP5). DL_MESO can simulate condensed phases using the Lattice-Boltzmann Equation, Dissipative Particle Dynamics and Smoothed Particle Hydrodynamics.

• DL_POLY   Molecular Dynamics

  • DL_POLY is a package of subroutines, programs and data files, designed to facilitate MD simulations of macromolecules, polymers, ionic systems and solutions on a distributed memory parallel computer. This package is free for UK academics.

• DL Visualize   3D Viewer, Quantum Mechanics, Crystallography

  • DL Visualise provides a powerful interface for constructing and visualizing crystals, surfaces and molecules and their properties. It has interfaces to CRYSTAL, DX_EXCURV and GULP.

• DMax Chemistry Assistant   Cheminformatics

  • DMax Chemistry Assistant automatically finds, formulates and shows scientific hypotheses that best match observations in a high-throughput screen. It also makes a statistical estimate of the confidence you can have in each hypothesis, and it can predict unmeasured values based on past measurements.

• Dockres   Docking

  • Dockres reads the log file of docking runs performed by Autodock and extracts the top scoring poses subject to various filters. The program also calculates distributions of various properties of the ligand set (e.g. molecular weight, number of hydrogen bond donors) and the distribution of docking sites as well as the distribution of docking free energies per target residue.

• Dragon   Cheminformatics

  • Dragon is an application for the calculation of molecular descriptors. These descriptors can be used to evaluate molecular structure-activity or structure-property relationships, as well as for similarity analysis and high-throughput screening of molecule databases

• DRAWxtl   Crystallography, 3D Viewer

  • DRAWxtl reads a basic description of the crystal structure, and displays it using polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fouier contours and the unit-cell boundary. Image information can be exported as Virtual Reality Modeling Language (VRML), and in a format suitable for the Persistence of Vision Ray Tracer (POV-RAY).

• EasyChem   2D Draw

  GPL, C

  • EasyChem is a program designed to draw chemical structures, written under Linux and using Gtk+. Its main features are ease of drawing ornaments (non-bonding electron pairs, etc.) and EPS exporting with LaTeX fonts.

• Ecce   Quantum Mechanics, 3D Viewer

  • Ecce (the Extensible Computational Chemistry Environment) provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies.

• EChem++   Electrochemistry

  GPL, C++

  • EChem++ is designed to be used for the modeling and simulation of (electro)chemical reaction kinetics as well as transport processes. Hardware control of experiments and data analysis are future aspects of the project.

• Eden   Crystallography

  GPL, C

  • Eden (short for Electron DENsity) implements the 'holographic' method of recovering the electron density in a crystal. The most unconventional feature of the holographic method is that it is a real-space method: it searches for a distribution of electrons in the unit cell that meets all the known constraints on the molecules themselves, while giving rise to the observed diffraction pattern.

• EGO   Molecular Dynamics

  GPL, C

  • EGO is a parallel program for molecular dynamics simulations of biomolecules. The program computes molecular dynamics trajectories. It uses a multiple time step algorithm combined with a structure adapted fast multipole method for the description of long range electrostatics. The method has been demonstrated to scale linearly with the number of atoms in the range of about 40,000 atoms.

• eHiTS   Docking

  • eHiTS (Electronic High Throughput Screening) is a program for flexible docking of ligands to proteins. It is fast, fully automated, and comprehensively covers the searc space.

• Ergo   Quantum Mechanics

  GPL, C++

  • Ergo is a quantum chemistry program for large-scale self-consistent field calculations. It performs electronic structure calculations using Hartree-Fock and Kohn-Sham density functional theory using Gaussian basis sets. Linear scaling techniques are employed such as fast multipole methods, hierarchic sparse matrix algebra, density matrix purification, and efficient integral screening.

• Erkale   Quantum Mechanics

  GPL, C++

  • ERKALE is a quantum chemistry program used to solve the electronic structure of atoms, molecules and molecular clusters. The main use of ERKALE is the computation of x-ray properties, such as ground-state electron momentum densities and Compton profiles, and core (x-ray absorption and x-ray Raman scattering) and valence electron excitation spectra of atoms and molecules.

• Espoir   Crystallography

  GPL, Fortran

  • Espoir solves crystal structures from powder diffraction data using the direct space approach.

• ESPResSo   Molecular Dynamics, Mesoscopic modeling

  GPL, C

  • ESPResSo (Extensible Simulation Package for Research on Soft matter) is a software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research, with emphasis on charged systems. It can be driven by Tcl scripts.

• Fenske-Hall program   Quantum Mechanics

  • an Hartree-Fock SCF method (STO Basis Set), with special optimization, suitable to perform calculations (especially ionization energies) of large inorganic and organometallic compounds. The original FORTRAN source is compiled by f2c.

• FHI98md   Quantum Mechanics

  • FHI98md is an efficient code to perform density functional theory total-energy calculations for materials ranging from insulators to transition metals. The package employs first-principles pseudopotentials, and a plane-wave basis-set.

• FIRM   NMR

  • FIRM (Full Iterative Relaxation Matrix) a flexible program for calculating NOEs and back-calculated distance constraints using the full relaxation matrix approach.

• fityk   Crystallography, Spectroscopy

  GPL, C++

  • fiytk is a tool for curve fitting and data analysis (e.g. baseline correction), used in crystallography, chromatography, photoluminescence or photoelectron spectroscopy, infrared or Raman spectroscopy, and in other fields. Common tasks can be automated with scripts.

• FlexV   3D Viewer, Docking

  • FlexV is a general-purpose molecular viewer. It is a stand-alone tool with easy interfaces, and can be used in combination with any kind of molecular modeling software, although originally designed as a visualisation front-end for FlexX.

• FOX   Crystallography

  GPL, C++

  • FOX performs ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Solutions can be constrained using angle or atom based constraints. Multiple powder patterns can be used simultaneously, and input is using a graphical user interface.

• Frowns   Cheminformatics

  Python Software Foundation License, Python

  • Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry-related algorithms.

• Gabedit   Quantum Mechanics, 3D Viewer

  BSD-like, C

  • Gabedit is a graphical user interface for Molpro, Molcas, MPQC and Gaussian written in C,and based on GTK+.

• GAMESS   Quantum Mechanics

  • The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. Briefly, GAMESS can compute wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available for some of these. Analytic gradients are available for these SCF functions, for automatic geometry optimization, transition state searches, or reaction path following.

• GAMESS-UK   Quantum Mechanics

  • GAMESS-UK is a general purpose ab initio molecular electronic structure program for performing SCF-, DFT- and MCSCF-gradient calculations, together with a variety of techniques for post Hartree Fock calculations. The program is derived from the original GAMESS code, obtained from Michel Dupuis in 1981, and has been extensively modified and enhanced sincce then. Available for free to U.K. academics.

• GAMGI   3D Viewer

  (GPL,BSD), (C,Python,Perl)

  • GAMGI (General Atomistic Modelling Graphic Interface) is an object-oriented program aiming to handle all aspects directly related with building, viewing and analysing atomic strucures, such as molecules, crystals, glasses, liquids, etc.

• GAMMA   NMR

  • GAMMA is a C++ library written for simulation of Magnetic Resonance experiments. Its purpose is to provide a simple and intuitive means with which users may construct simulation programs to suit their individual needs. A Python wrapper is also available.

• garlic   3D Viewer

  GPL, C

  • Garlic is a free molecular visualization program written for both educational and professional research purposes.

• Gaussian   Quantum Mechanics

  • Gaussian is an ab initio electronic structure program. Designed to model a broad range of molecular systems under a variety of conditions, it performs its computations starting from the basic laws of QM.

• GaussSum   Quantum Mechanics, Utility

  GPL, Python

  • GaussSum is a GUI application that can analyse the output of Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), and PC-GAMESS calculations to extract and calculate useful information. This includes the progress of the SCF cycles, geometry optimisation, UV-Vis/IR/Raman spectra, MO levels, MO contributions and more.

• GChemPaint   2D Draw

  GPL, C++

  • GChemPaint is a 2D chemical structures editor for the Gnome-2 desktop. GChemPaint is a multi document application and is a bonobo server so that chemistry can be embedded in other Gnome applications.

• GDIS   Crystallography, 3D Viewer

  GPL, C

  • GDIS (GTK Display Interface for Structures) is a visualization program for small molecules, crystals, and solution cells. It has support for common crystallographic file formats, and assorted tools for visualization (including diffraction pattern generation), manipulation, and model creation. Rendering of molecules and energy minimization are also possible via Povray and GULP.

• gdpc   3D Viewer, Molecular Dynamics

  GPL, C

  • gdpc is a program for visualising MD simulations. It is a very versatile program and could easily be used for other purposes. gdpc reads xyz input and custom formats and can write out pictures of the frames.

• gElemental   Cheminformatics, Education, Periodic Table

  GPL, (C++, Python)

  • gElemental is a periodic table viewer derived from GPeriodic that provides detailed information on the chemical elements. It uses the GTK+ toolkit and is available for Linux and other GTK+ platforms. It also provides Python bindings to the data, which is stored in a separate data library.

• GenChemLab   Education

  GPL, C++

  • GenChemLab (General Chemistry Lab Simulator) is a graphical application for simulating several common general chemistry exercises. It is meant to be used to help students prepare for actual lab experience.

• Ghemical   Quantum Mechanics, 3D Viewer

  GPL, C++

  • Ghemical is a computational chemistry software package with GUIs for both GLUT and GTK+, and some nice 3D-visualization tools. It can do "all atoms" molecular mechanics and dynamics, as well as quantum mechanics (ab initio and semi-empirical) models. It hopefully offers a good framework for a generic freeware molecular modeling tool.

• Ghemical-GMS   Quantum Mechanics, 3D Viewer

  GPL, C++

  • Ghemical-GMS is a specialized version of Ghemical developed for GAMESS. Ghemical-GMS contains an extra set of menus for creating GAMESS input files, and allows for the submission and queuing of GAMESS jobs using the GTK-Gamess program.

• Gibbs   Thermodynamics

  • Gibbs perfoms Gibbs-ensemble simulations with cavity-biased insertion to determine the densities of coexisting liquid and vapor phases in equilibrium with each other.

• Gnome Chemistry Utils   3D Viewer, UItilities

  LGPL, C++

  • The Gnome Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry. They are used both both in Gnome Crystal and GChemPaint.

• Gnome Crystal   Crystallography, 3D Viewer

  GPL, C++

  • Gnome Crystal is a lightweight model visualiser for crystal structures.

• Gnu Xtal System   Crystallography

  GPL, Fortran

  • The Gnu Xtal System is a package of over sixty crystallographic programs for calculations ranging from the reduction of raw diffraction intensities, to the solution, refinement and publication of crystal structures. These are applicable to X-ray, neutron and electron diffraction analyses, including charge density studies. The package contains interactive graphics tools.

• GOLD   Docking

  • GOLD is a program for calculating the docking modes of small molecules into protein binding sites as part of a virtual screening application. Docking is performed using a genetic algorithm and incorporates full ligand flexibility and partial protein flexibility. The GoldScore and ChemScore scoring functions are available, or a custom scoring function can be implemented. Cavity-bound waters and constraints can be included as part of the docking procedure.

• gOpenMol   Quantum Mechanics, 3D Viewer, Molecular Dynamics

  • gOpenMol is a graphics interface to the OpenMol set of programs, but can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials from many programs.

• GPeriodic   Periodic table

  GPL, C

  • GPeriodic is a periodic table application for Linux. It allows you to browse through a periodic table of the elements and view detailed information on each of the elements on each of the elements. 118 elements are currently listed.

• GRAMM   Docking

  • GRAMM (Global Range Molecular Matching) is a program for protein-protein and protein-ligand docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules. The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules.

• GRID   Cheminformatics, Docking

  • GRID is a computational procedure for determining energetically favourable binding sites on molecules of known structure. It may be used to study individual molecules such as drugs, molecular arrays such as membranes or crystals, and macromolecules such as proteins, nucleic acids, glycoproteins or polysaccharides.

• GRINSP   Crystallography

  GPL, Fortran

  • GRINSP is a Monte Carlo code (FORTRAN) for the prediction of inorganic structures built up from defined polyhedra.

• GROMACS   Molecular Dynamics

  GPL, (C, assembly, Fortran)

  • GROMACS is a versatile package for performing molecular dynamics. Some features of the software: standard MD simulations, energy minimizations, NMR refinement using NOE data, high performance due to well optimized code and smart algorithms, automatic topology generation from a building block library, flexible force field usage, non-equilibrium MD, many analysis and preprocessing tools.

• GROMOS   Molecular Dynamics

  • GROMOS is a general-purpose MD computer simulation package for the study of biomolecular systems (simulation of arbitrary molecules in solution or crystalline state, energy minimisation and analysis of conformations).

• GTK-Gamess   Quantum Mechanics, 3D Viewer

  GPL, C++

  • GTK-Gamess is a frontend to GAMESS that allows users to queue up GAMESS calculations and run them sequentially.

• GULP   Crystallography, Solids

  • GULP performs a variety of types of simulation on 3D periodic solids, gas phase clusters and isolated defects in a bulk material. In particular GULP is designed to handle both molecular solids and ionic materials through the use of the shell model. One difference between GULP and other similar programs is that symmetry is used for solids to accelerate the calculations and to simplify the input.

• HKL Package   Crystallography

  • The HKL Package is a suite of programs for the analysis of X-ray diffraction data collected from single crystals. It consists of three parts: XdisplayF for visualization of the diffraction pattern, Denzo for data reduction and integration, and Scalepack for merging and scaling of the intensities obtained by Denzo or other programs.

• HONDOPLUS   Molecular Dynamics

  • HONDOPLUS is a version of HONDO 99.6 with additional modules for evaluating Löwdin and CM2 partial atomic charges and for carrying out SM5.42R continuum solvation calculations by Hartree-Fock and hybrid DFT-Hartree-Fock methods.

• ICM Browser   3D Viewer

  • ICM Browser is a program for molecular modeling and high-performance molecular visualization and animation. A commercial version, ICM Browser Pro, has additional capabilities relating to creating, storing and sharing structural, biological and chemical information.

• Indigo   Cheminformatics

  GPL, C++

  • Indigo is a cheminformatics toolkit that includes a rendering library (Dingo), generation of canonical SMILES (Cano), an Oracle cartidge for searching molecular databses (Bingo) and R-Group deconvolution (Deco). It also can handle nucleotides (Nucleo).

• Intocham   Molecular Mechanics, Molecular Dynamics

  • Intocham converts from InsightII .car format to Charmm, Amber or Moil formats.

• Isotopic Pattern Calculator   Mass Spectrometry

  GPL, C

  • Isotopic Pattern Calculator is a small tool for mass spectrometry. It calculates the isotopic distribution for a given chemical formula or peptide sequence. Furthermore, it can use Gnuplot to visualise the results.

• Jaguar   Quantum Mechanics

  • Jaguar is an ab initio electronic structure software package that provides chemical accuracy for realistic systems, with particular strength in treating metal-containing systems. Calculations are efficient and scale well with molecular size.

• Jana2000   Crystallography

  • Jana2000 is a system for solving and refinement of regular, modulated and composite structures from monocrystal and powder diffraction data.

• JChem   Cheminformatics

  • JChem is a Java tool for developing applications that manipulate mixed chemical and corporate data. It supports most operating systems, database handlers, and web servers. JChem is an excellent tool for developing distributed custom chemical applications that can be accessed by web browsers.

• JChemPaint   2D Draw

  LGPL, Java

  • JChemPaint is a Java program for drawing 2D chemical structures. It can load and save in CML format, export as bitmap and SVG, and automatically layout structures.

• JMap3D   3D Viewer

  • JMap3d takes volumetric data (particularly electron density data) and polygonises them, in order to produce up to five iso-surfaces. The result is written to a VRML97 (VRML2.0) file, which can then be viewed with any VRML viewer of your choice or with the included Java3D VRML viewer (from the Java3D & VRML working group).

• JME Molecular Editor   2D Draw

  • JME Molecular Editor is a Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page. Editor can generate SMILES or MDL mol file of created structures.

• Jmol   3D Viewer, Quantum Mechanics

  LGPL, Java

  • Jmol is a Java-based molecule viewer that has been developed as a cross-platform replacement for the Chime plugin. Available as an applet for web pages or as a stand-alone application. It can read multiple file formats, create animations, show molecular vibrations, and supports the Chime scripting language.

• JMolEditor   3D Viewer, Quantum Mechanics

  • JMolEditor is a Java-based molecular viewer for quantum chemistry calculations, with support for Gaussian, GAMESS, ADF and Q-Chem calculations. Molecules can be built, and input files can be prepared and submitted. Calculation results, including isosurfaces from cube files, can be displayed.

• JOELib   Cheminformatics

  GPL, Java

  • JOELib is a Java library for cheminformatics. Among its many features, it can perform SMARTS substructure searches, calculate descriptors, and read and write molecular file formats including Chemical Markup Language.

• JSV   3D Viewer, Crystallography

  • JSV (Java Structure Viewer) is a crystal structure viewer written in Java. It can also calculate X-ray diffraction intensities. The diffraction viewer module XRDL allows the 3D/2D display of the diffraction pattern. This software is 'Charityware'.

• Kalzium   Education, Periodic Table

  GPL, C++

  • Kalzium is an application which will show you some information about the periodic system of the elements. It is included in KDE 3.1. A balanced equation solver, eqchem, is also part of Kalzium.

• Kemistry   2D Draw, 3D Viewer, Utility

  GPL, C++

  • Kemistry is a collection of chemistry-related applications written for the KDE2. The Kemistry package provides three applications: KMolCalc - a molecular weight calculator; KDrawStruct - a 2D structures editor; KMolViewer - a 3D molecular renderer. All Kemistry applications are still in their early development stages.

• Khimera   Quantum Mechanics, Reactions, Thermodynamics

  • Khimera is a software tool for the estimation of thermodynamic properties and kinetic rate parameters based on results of quantum-chemical calculations (supports GAMESS, Gaussian, Jaguar, ADF). Reactor models included in KHIMERA help to create and test the mechanism of chemical processes.

• Kintecus   Reactions

  • Kintecus is modeling software to simulate the chemical kinetics of combustion, nuclear, catalyst reactor, and enzyme reactions.

• KMovisto   3D Viewer

  GPL, C++

  • KMovisto is a molecular viewer. It can import GAUSSIAN 94 or 98 files, and XYZ files. 3D view modes (anaglyph or stereo pair) make it possible to enjoy stereoscopic impressions of the molecular structure. In addition, KMovisto can export export POV-Ray files for rendering high quality presentations, as well as VRML files for 3D presentations on the world wide web.

• KryoMol   3D Viewer, Quantum Mechanics, Molecular Mechanics, Molecular Dynamics, NMR

  GPL, C++

  • KryoMol is a KDE-based program for visualisation and analysis of several chemistry related file types such as quantum chemistry log files (Gaussian, NWChem, ACESII, GAMESS), molecular mechanics log files (Tinker, Macromodel), 1-D NMR spectra and JCAMP-DX spectra.

• LAMMPS   Molecular Dynamics

  GPL, C++

  • LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics (MD) code created for simulating molecular and atomic systems such as proteins in solution, liquid-crystals, polymers, zeolites, or simple Lennard-Jonesium.

• LaTeX Chemistry Packages   LaTeX

  • Chemistry packages for using with the document typesetting system LaTeX. Includes packages for reactions, molecular formulae, R and S codes, chemistry journals, symmetry elements and even to draw chemical structures.

• LaueX   Crystallography

  • LaueX is an interactive program with a GUI that can simulate a Laue diagram, when given the orientation of the crystal and the cell parameters. LaueX can also index a Laue diagram if the position of experimental spots are provided.

• Lennard-Jones Gas Simulation   Gas simulation

  GPL, C++

  • The Lennard-Jones Gas Simulator does a molecular simulation of noble gases.

• Linux for Chemistry   Software Collection

  • The Linux for Chemistry project (LfC) is dedicated to compiling the most comprehensive collection of Chemistry software, and making it available for the Linux operating system. LfC provides point-and-click installation, a complete on-line library of searchable documentation, and much more.

• LSD Software   NMR, Utility

  GPL, C

  • The goal of LSD (Logic for Structure Determination) is to help the user propose one or more molecular structures from data that is mainly extracted from 2D NMR spectra.

• MacroModel   Molecular Mechanics, Molecular Dynamics

  • MacroModel is a molecular modeling software package which allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.

• Maestro   3D Viewer

  • Maestro is the unified interface for all Schrodinger software. Impressive rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers.

• MAPS   3D Viewer, Quantum Mechanics, Molecular Dynamics

  • MAPS (Materials And Processes Simulations) is a platform for performing materials modeling and simulations. It provides a flexible framework for accessing both proprietary and open-source simulation codes in the areas of quantum, classical, mesoscale and chemical engineering. MAPS serves as an integration tool for all modeling related tasks and data and offers a multi-user/multi-project modeling environment complete with data management.

• Marvin   Cheminformatics, 2D Draw

  • Marvin is a suite of Java based chemistry software that have different forms: 1. Marvin Applets are made for the Web Developer who builds chemistry-related World Wide Web sites; 2. Marvin Beans are made for the Software Developer who wants to incorporate molecule drawing or visualizing capabilities into his/her application; 3. MarvinSketch is an application for the Chemist or anyone else who wants to draw chemical structures.

• massXpert   Mass spectrometry

  GPL, C++

  • massXpert lets users analyse/predict mass spectrometric data on (bio)polymers. Notable features include ex nihilo polymer chemistry definitions, highly sophisticated editing of polymer sequences and chemical reaction simulations.

• MAUD   Crystallography

  • MAUD (Material Analysis Using Diffraction) is a general diffraction/reflectivity analysis program mainly based on the Rietveld method. It has a GUI, and a wide range of features including ab initio structure solution, various optimisation algorithms, Le Bail fitting and microstruture analysis.

• Maxwell   Quantum Mechanics, Crystallography

  • Maxwell consists of a suite of programs that implement the Maxwellian formalism for calculating the interaction energy between charge distributions as represented by the multipole expansion. It can also be applied to crystal lattices.

• MCCCS Towhee   Molecular Dynamics

  GPL, (C, Fortran)

  • MCCCS Towhee is a Monte Carlo molecular simulation code which can be used for the prediction of fluid phase equilibria using a wide variety of atom-based force fields and several ensembles (Gibbs, Canonical, Isobaric-isothermal and Grand Canonical). It has also been extended for use with solid (or porous) phases.

• McMaille   Crystallography

  GPL, Fortran

  • McMaille is a program for indexing powder diffraction patterns by Monte Carlo and grid search.

• MCPRO   Molecular Dynamics

  • MCPRO performs Monte Carlo statistical mechanics simulations of peptides, proteins, and nucleic acids in solution; it was derived from BOSS, but makes extensive use of the concept of residues. Free energy changes can be computed via FEP calculations and have been used extensively for studying protein-ligand binding.

• MCTDH   Quantum Mechanics

  • MCTDH (Multi Configuration Time Dependent Hartree) is a general algorithm to solve the time-dependent Schrödinger equation for multidimensional dynamical systems consisting of distinguishable particles. MCTDH can thus determine the quantal motion of the nuclei of a molecular system evolving on one or several coupled electronic potential energy surfaces. MCTDH can also be used to propagate density operators and to determine eigenvalues and eigenstates of a molecular vibrational Hamiltonian.

• MDTools   Molecular Dynamics

  • MDTools is a collection of programs, scripts, and utilities to make various molecular dynamics tasks easier, and to provide basic code and utilities which can be built up into larger toolsets.

• Mercury   Crystallography, 3D Viewer

  • Mercury is a program for visualising crystal structures in three dimensions. Its features include:The ability to load hit lists from ConQuest searches, or to browse the entire Cambridge Structural Database, or to read in crystal structures in various formats. The ability to rotate and translate the 3D crystal-structure display, and to view down cell axes, reciprocal cell axes, and the normals to least-squares and Miller planes. The ability to measure and display distances, angles and torsion angles by atom picking and much more.

• MetaStudio   Quantum Mechanics, 3D Viewer

  GPL, Java

  • MeTA Studio is programmable IDE tailored for a computational chemist. It has support for BeanShell and Jython, and integrates Jmol.

• MEXICO   NMR

  GPL, C

  • MEXICO simulates the NMR lineshapes of coupled spin systems undergoing chemical exchange. It will simulate systems and, if experimental data are available, it will perform an iterative fit to give optimized values of the parameters.

• MGLTools   Docking, 3D Viewer, Cheminformatics

  • MGLTools is a suite of software including PMV (Python Molecular Viewer), a molecule viewing and manipulation environment, ADT (AutoDockTools) for looking at AutoDock results, and pyBabel, a Python re-implementation of some of the features of Babel v1.6.

• Mindy   Molecular Dynamics

  • Mindy is a very simple, serial molecular dynamics program derived from NAMD source code. It currently uses xplor parameter and structure files.

• MMC   Thermodynamics

  • MMC is a Metropolis Monte Carlo program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, extension-biased and local torsion changes, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change).

• MMTK   Molecular Dynamics

  CeCILL, Python

  • MMTK (the Molecular Modelling Toolkit) is a program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations.

• Mnova Suite   NMR

  • Mnova Suite is a GUI with plugins for processing and reporting NMR data, predicting NMR data and processing MS data. Individual plugins are available separately.

• ModelFree   NMR

  GPL, Fortran

  • ModelFree is a program for optimizing Lipari-Szabo model free parameters to heteronuclear NMR spin relaxation data.

• MOE   Cheminformatics

  • MOE (Molecular Operating Environment) can be used to manipulate and analyse large collections of compounds in a spreadsheet-like environment. It can be used to calculate descriptors, for building QSAR/QSPR models, for similarity searching and diverse subset selection, conformational searching and 3D pharmacophore searching. It has an embedded scripting language, SVL (Scientific Vector Language).

• Molaris   Enzyme reactions and properties

  • Includes POLARIS and ENZYMIX in a unique package with an interface. Enzymix is a macromolecular simulation program designed to study the functions of proteins. Polaris is a fast converging computational software based on the Protein Dipoles - Langevin Dipoles (PDLD) approach.

• MOLCAS   Quantum Mechanics

  • MOLCAS allows an accurate ab initio treatment of very general electronic structure problems for molecular systems in both ground and excited states. MOLCAS contains a number of codes that can perform such calculations (MP2, CC, CPF, CCSD(T) etc.). It can also treat highly degenerate states using general and effective multiconfigurational SCF calculations at the CASSCF level, as well as RASSCF.

• MOLDA for Protein Modeling   3D Viewer, Quantum Mechanics

  • MOLDA is a molecular modeling program. 3D molecular structures in VRML and POV-Ray formats can be generated using the output from a variety of computational chemistry programs.

• Molden   3D Viewer, Quantum Mechanics

  • MOLDEN is a package for displaying molecules, electron density, and orbitals from ab initio and semi-empirical packages. It has a powerful Z-matrix editor.

• Moldy   Molecular Dynamics

  GPL, C

  • Moldy is a general-purpose molecular dynamics simulation program. It is sufficiently flexible that it ought to be useful for a wide range of simulation calculations of atomic, ionic and molecular systems.

• Molegro Molecular Viewer   3D Viewer

  • Molegro Molecular Viewer is a free cross-platform application for visualization of molecules and analysis of protein-ligand interactions.

• Molegro Virtual Docker   Docking

  • Molegro Virtual Docker is an integrated platform for predicting protein-ligand interactions. It handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands.

• MOLEKEL   3D Viewer, Quantum Mechanics

  • MOLEKEL is an interactive, three-dimensional molecular graphics package. MOLEKEL represents molecules,it can superimpose molecules, calculates and displays isosurfaces of electron and spin densities as well as molecular orbitals from the output of various electronic structure calculation programs. MOLEKEL can animate and display vibrational modes, animate geometry optimizations and multiple coordinate PDB and XYZ files.

• Mollie   Database

  GPL, Perl

  • Mollie is a small web-oriented database for molecular information. It uses Perl for CGI, and PostgreSQL.

• MOLMOL   3D Viewer

  • MOLMOL is a program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.

• Molpro   Quantum Mechanics

  • Molpro is a system of ab initio programs for molecular electronic structure calculations. with an emphasis on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. Using recently developed integral-direct local electron correlation methods, accurate ab initio calculations can be performed for much larger molecules than with most other programs.

• MolScript   3D Viewer

  • MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations. It also produces output files that can be used in Raster3d.

• molsKetch   2D Draw

  GPL, C++

  • molsKetch is a molecular drawing tool for 2D molecular structures. Its goal is to help you draw molecules quick and easily. As well as allowing the user to export high quality images in a number of vector and bitmap formats, it can read and write multiple chemical file formats (using the Open Babel library). molsKetch features intelligent addition/removal of hydrogen atoms and a built-in library that provides quick access to regularly used molecules and functional groups.

• MolSurfer   3D Viewer, Enzyme

  • MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structure. MolSurfer can be used to study protein-protein and protein-DNA/RNA interfaces.

• Mol_Volume   Molecular volume

  • Mol_Volume calculates the volume of a macromolecule by a method somewhat akin to the Monte Carlo method, namely, by measuring how many vertices of a dense regular grid happen to be within the probe radius of the molecule's atoms.

• MOPAC 7   Quantum Mechanics

  Public Domain, Fortran

  • MOPAC is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. The semi-empirical Hamiltonians MNDO, MINDO/3, AM1, and PM3 are used in the electronic part of the calculation to obtain molecular orbitals, the heat of formation and its derivative with resperivative with respect to molecular geometry.

• MOPAC 2007   Quantum Mechanics

  • MOPAC2007 is a general-purpose semiempirical quantum mechanics package for the study of chemical properties and reactions in gas, solution, or solid-state. MOPAC2007 can be used to directly predict numerous chemical and physical properties, such as Gibbs free energies, activation energies, reaction paths, dipole moments, non-linear optical properties, and infrared spectra. It is based on the public domain MOPAC 7.

• MOSCITO   Molecular Dynamics

  GPL, Fortran

  • MOSCITO is designed for molecular dynamics simulations of condensed phase systems defined by classical molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS.

• moviemol   3D Viewer, Molecular Dynamics

  • Moveiemol is a program for visualization and animation of molecular structures. Moviemol typically takes sets of molecular coordinates and displays each of these sets or frames one after the other to create a movie. The molecules/atoms/ions are displayed in ball-and-stick form. At any moment during the animation, the molecules can be rotated or translated, magnified or diminished. The program also produces very nice postscript images of publication quality.

• MPQC   Quantum Mechanics

  LGPL, C++

  • MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. It runs on a wide range of architectures ranging from individual workstations to symmetric multiprocessors to massively parallel computers. Its design is object oriented, using the C++ programming language.

• MSMS   Molecular surface

  • MSMS stands for Michel Sanner's Molecular Surface, or Maximal Speed Molecular Surface. It allows the user to compute very efficiently triangulations of solvent excluded surfaces.

• MULTIMODE   Quantum Mechanics

  • MULTIMODE performs Vibrational Self Consistent Field (VSCF) and several types of "CI" calculations for the rovibrational energies and wavefunctions of polyatomic molecules, transition states, clusters, etc. The code is based on the Watson Hamiltonian for non-linear molecules.

• Music   Molecular Dynamics

  GPL, Fortran

  • Music (Multi-purpose SImulation Code) is an object-oriented package intended to perform various types of Molecular Dynamics and Monte Carlo simulations with user-specified forcefields. It can be used to simulate diffusion and adsoprtion in zeolites, for liquid and gas simulations as well, and may be easily extended for solid simulations.

• NAB   Molecular Dynamics, Molecular Mechanics

  GPL, C

  • NAB (Nucleic Acid Builder) is a computer language (specified through lex and yacc) that allows nucleic acid structures to be described in a hierarchical fashion, using a language similar to C or awk, but designed especially for the manipulation of nucleic acid structures.

• Naccess   Solvent accessibility

  • Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids.

• NAMD   Molecular Dynamics

  • NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

• NAMOT   3D Viewer

  • NAMOT (Nucleic Acid MOdeling Tool) is a graphic tool to build and manipulate nucleic acid structures.

• nMOLDYN   Molecular Dynamics

  CeCILL, Python

  • nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.

• NMRPipe   NMR

  • The NMRPipe software package consists of a series of standalone programs such as NMRPipe (spectrometer data conversion, advanced multidimensional data processing), NMRDraw (graphical interface for most package tools, interactive processing, script editing interface, time domain data inspection, real-time phasing, automated peak detection, spectral analysis), NMRWish (custom version of Tcl/Tk for spectral analysis, spectral database engine, communication between applications), DC (dipolar coupling and chemical shift analysis) and a multitude of spectral analysis tools.

• NMR-SHARC   NMR, Quantum Mechanics, Cheminformatics

  • NMR-SHARC is a cooperative, platform-independent, program-independent archving system for ab initio NMR chemical shift calculations.

• NMRShiftDB server   NMR, Cheminformatics

  GPL, Java

  • The NMRShiftDB server is open source software which can be used to maintain a local repository of the results of NMR experiments. This software was developed for the NMRShiftDB database, an open-source, open-access, open-submission, open-content web database for chemical structures and their associated nuclear magnetic resonance data.

• NMRViewJ   NMR

  • NMRViewJ is a program for the visualization and analysis of NMR datasets. Some of its features are: unlimited number of spectral windows and data files; contour and 1D vector plots of any plane of any 2, 3, or 4 dimensional spectra; automatic peak picking, searching, facilitated analysis and interactive peak editing; powerful command language and programmable user interface; NOE constraint generation and analysis.

• NWChem   Quantum Mechanics

  ECL, (Fortran, C, C++)

  • NWChem is a computational chemistry package designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources.

• O   3D Viewer, Crystallography

  • O is a general purpose macromolecular modelling environment. The program is aimed at scientists with a need to model, build and display macromolecules, particularly in the context of crystallography..

• Olex2   3D Viewer, Crystallography

  • Olex2 is an easy-to-use program for small-molecule structure solution and refinement. It also includes many useful tools for structure analysis, archiving and report generation. All aspects of the structure determination and publication process are presented in a single, workflow-driven package - with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.

• Open Babel   Cheminformatics

  GPL, (C++, Perl, Python, Java, Ruby)

  • Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. It provides a command-line interface (babel), a programming library (libopenbabel), as well as bindings to several languages such as Python, Perl, Ruby and Java.

• OpenChrom   Mass Spectrometry, Spectroscopy

  Eclipse Public License, Java

  • OpenChrom is a cross-platform GUI for chromatography and mass spectrometry. It is able to import binary and textual chromatographic data files, such as *.D chromatograms from Agilent Technologies or NetCDF. A basic set of methods to detect baselines, peaks and to integrate peaks in a chromatogram are implemented. Preprocessing steps, e.g. To remove certain mass fragments (m/z) such as nitrogen (28) or water (18), are supported by applying filters on the chromatogram or mass spectrum. Extensions are welcome, as OpenChrom is open source and uses a flexible approach, which allows others to implement their own methods, algorithms, filters, detectors or integrators.

• open enventory   Cheminformatics

  AGPL, (Javascript, PHP)

  • open enventory is an integrated laboratory journal and inventory program. It is a web application that runs in your browser. Automatic acquisition of freely accessible data from online databases makes manual data acquisition and catalogue searches obsolete, and price surveys can be done with a mouseclick. The laboratory journal uses the information available in the inventory database and makes the data available for all members of a workgroup. Both inventory and laboratory journal have the ability to allow data exchange between workgroups.

• OpenMol   Quantum Mechanics

  • OpenMol is a quantum chemical software package: it is an integrated program for electronic structure and property calculations of molecules. User guidance, the evaluation and interpretation of results and computer based learning are the three unique features of OpenMol that distinguish it from all other programs in the field. The concept of OpenMol is based on the fundamental ideas of two software concepts, the (rule based) expert system and the abstract data type model.

• OpenMX   Quantum Mechanics, Materials

  GPL, C

  • OpenMX (Open source package for Material eXplorer) is a program for nano-scale material simulations, which is designed for the realization of large-scale ab initio calculations based on a density functional theory (DFT) , norm-conserving pseudopotentials, and pseudo atomic localized basis functions.

• OpenThermo   Thermodynamics

  GPL, C++

  • OpenThermo is a program package for statistical thermodynamics computations beyond rigid rotor harmonic oscillator approximation (RRHOA), with taking into account internal rotations and vibration anharmonicity. In contrast to statistical subprograms integrated to QC packages, OpenThermo is designed to make the calculation transparent to user and give maximum control under the choice of used theories and approximations.

• ORAC   Molecular Dynamics

  GPL, Fortran

  • ORAC is a molecular dynamics program for running classical simulations of solvated biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles using multiple time steps integrators. Electrostatic interactions may be handled through the Smooth Particle Mesh Ewald method.

• Orbdraw   Quantum Mechanics, 3D Viewer

  • Orbdraw is a visualization program for displaying molecular orbital and electron density data from Gaussian, Gamess, Jaguar, Hondo, Mopac or Ampac calculations. Orbdraw can display the molecular orbitals, electron densities or spin densities in 3D as either wire frames or solid surfaces and can map orbitals or charges onto the density surfaces.

• ORCA   Quantum Mechanics

  • The program ORCA is a modern electronic structure program package with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to correlated ab initio methods. It can also treat environmental and relativistic effects.

• ORTEP   Crystallography

  • ORTEP (Oak Ridge Thermal Ellipsoid Plot) is a program for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoin probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. There is also a Linux-specific Linux ORTEP page.

• OS-ELN   Electronic Lab Notebook

  • OS-ELN (Open Source Electronic Lab Notebook) will be of particular interest to Universities and Colleges needing a simple, low-cost ELN to be used by their students in classes. The system is easily and cost effectively deployed, and can be expanded and modified as needed.

• OSET   Reactions, Education

  GPL, Java

  • OSET (Organic Synthesis Exploration Tool) is a computer-assisted organic synthesis (CAOS) program for the retrosynthetic analysis of target molecules. Intended for educational use, as a tool for learning chemical synthetic design at undergraduate organic chemistry courses.

• OVITO   3D Viewer, Molecular Dynamics, Materials

  GPL, C++

  • OVITO (Open Visualization Tool) allows the analysis and visualization of large-scale atomistic datasets produced by molecular dynamics/statics and Monte-Carlo simulation codes.

• Packmol   Molecular Dynamics

  • Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

• PaDEL-Descriptor   Cheminformatics, QSAR

  GPL, Java

  • PaDEL-Descriptor is a GUI for calculating molecular descriptors and fingerprints. The software currently calculates 856 descriptors (722 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints. The descriptors and fingerprints are calculated using the Chemistry Development Kit with some additional descriptors and fingerprints. These additions include atom type electrotopological state descriptors, extended topochemical atom (ETA) descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth.

• Pallas   Cheminformatics

  • The Pallas suite includes software for predicting pKa (pKalc), logP (PrologP), logD (PrologD), toxicity values (HazardExprt) and metabolitic fate (MetabolExpert) based on structural formula of compounds.

• Pcmodel   Quantum Mechanics, 3D Viewer

  • Pcmodel is a molecular modeling package with interfaces to many quantum chemistry packages. It also includes support for geometry optimisation with various force fields as well as conformational searching.

• PDBCat   Cheminformatics

  University of Illinois Open Source License, C

  • PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc.

• pDynamo   Molecular Dynamics, Molecular Mechanics, Quantum Mechanics

  CeCILL, (C, Python)

  • pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions.

• Perl Chemistry Modules   Cheminformatics, 3D Viewer

  Artistic License, Perl

  • Perl extensions for working with chemical information, for example SMILES strings, molecular file formats, creation of VRML files, conversion to internal coordinates. See also PerlMol.

• PINY_MD   Molecular Dynamics, Quantum Mechanics

  Common Public License, C

  • PINY_MD is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations. Such capabilities include force-field based simulations on system ranging in complexity from simple molecular liquids and crystals to large biomolecular systems. In addition, PINY_MD can perform ab initio molecular dynamics and geometry optimization using plane-wave based generalized gradient (GGA) density functional based representations of the electronic structure combined with the Car-Parrinello propagation scheme.

• PLATON   Crystallography

  • PLATON is a versatile SHELX97 compatible multipurpose crystallographic tool. Most PLATON features complement those available in the excellent and widely distributed SHELX97 package for crystal structure determination and refinement.

• POLYRATE   Reactions

  • POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases).

• PovChem   3D Viewer

  • PovChem is a chemical visualisation and illustration program with a graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration, then exports the picture in POV-Ray format (high-quality images).

• PQS Ab Initio Module   Quantum Mechanics

  • PQS (Parallel Quantum Solutions) Ab Initio Module is a comprehensive program for electronic structure calculations. All major ab initio functionality is fully parallel.

• ProtoFit

  GPL, (Fortran, Tcl)

  • ProtoFit is a tool for optimization of surface protonation models from acid-base titration data. Although ProtoFit is designed with the analysis of the proton buffering behavior of surfaces in mind, it can be used equally well for other substances such as a dissolved acids that reversibly exchanges protons with water.

• PWscf   Quantum Mechanics

  GPL, Fortran

  • PWscf (Plane-Wave Self-Consistent Field) is a set of programs for electronic structure calculations within Density-Functional Theory and Density-Functional Perturbation Theory, using a Plane-Wave basis set and pseudopotentials.

• PyDespike   Raman, Spectra

  GPL, Python

  • PyDespike is a program to graphically process (ie. despike) Raman and other spectroscopic data. It reduces the tedium involved in removing spikes in data due to artificial background fluctuations.

• PyMOL   3D Viewer

  Python License, (C, Lua, Python, Tcl)

  • PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.

• PyQuante   Quantum Mechanics

  BSD, (Python, C)

  • PyQuante is an open source suite of programs for developing quantum chemistry methods, written in the Python programming language, but with many rate-determining modules written in C for speed. The resulting code is easy to understand and modify, providing a well-engineered set of tools so that scientists can construct their own quantum chemistry programs without going through the tedium of having to write every low-level routine.

• PyVib2   Quantum Mechanics

  GPL, Python

  • PyVib2 is a program for analyzing vibrational motion and vibrational spectra, written in pure Python. PyVib2 permits the automatic correlation of vibrational motions of molecules thereby allowing an understanding of Raman, Raman optical activity (ROA), infrared vibrational absorption (IR), and vibrational circular dichroism (VCD) spectra. Features include a Versatile representation of vibrational motions, visualization of Raman/ROA and IR/VCD generation in molecules and the production of publication quality spectra. It currently supports DALTON and Gaussian output files.

• Q-Chem   Quantum Mechanics

  • Q-Chem is a modern ab initio quantum chemistry software package capable of analyzing large structures in practical amounts of time without compromising accuracy.

• QikProp   Cheminformatics

  • QikProp provides rapid predictions for physically-significant descriptors and pharmaceutically-relevant properties of neutral organic molecules. Accurate predictions are made for free energies of solvation in hexadecane, octanol, and water, octanol/water partition coefficient (log P), aqueous solubility (log S), and Caco-2 cell permeabilty. Results for libraries of compounds are output in a format ready for facile incorporation into spreadsheet and QSAR programs.

• QMForge   Quantum Mechanics, 3D Viewer

  GPL, Python

  • QMForge is a program to analyze the results of quantum chemistry (DFT) calculations: Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), and PC-GAMESS files are supported. The following analyses are available for user-defined molecular fragments: Mulliken, C-squared and Overlap Population analyses, Fragment and Charge Decomposition Analyses.

• qmol   Utility

  GPL, C++

  • qmol is a simple molecular weight calculator, available for Linux and Windows. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %).

• QSite   Quantum Mechanics

  • QSite is a mixed mode QM/MM program for energy calculations of protein-ligand interactions in the active site.

• QTree   3D Viewer

  • QTree is a program for generating CPK, Ball and Stick and worms pictures of molecules using the quad-tree algorithm. This is a relatively fast method of generating near-photographic quality images though it does not generate shadows. A sense of depth is provided by darkening atoms farther away from the viewer.

• Quantum   Quantum Mechanics, Docking

  • Quantum is a pure physics based molecular docking software which calculates Kd of a protein-ligand complex, and ligand position in the protein active site. This enables virtual screening of compound libraries. The calculation takes into account metals and other hetatoms in the protein active site as well as protein flexibility.

• QuteMol   3D Viewer

  GPL, C++

  • QuteMol is an open source (GPL), interactive, high quality molecular visualization system that aims to improve clarity and provide an easier understanding of the 3D shape and structure of large molecules or complex proteins. Its features include real time ambient occlusion, depth-aware silhouette enhancement, and automatic generation of animated gifs of rotating molecules for web page animations.

• RasMol   3D Viewer

  GPL, C

  • RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

• RasMol-UCB   3D Viewer

  • UCB-Enhanced Rasmol is based on Rasmol 2.6 with enhancements added. These enhancements include: multiple molecules can be viewed, part of a molecule can be rotated around a bond, distances/angles can be measured and the labels displayed.

• Raster3D   3D Viewer

  • Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.

• Rave   Crystallography

  • Rave is a suite of programs for single and multiple domain, single and multiple crystal real-space electron-density averaging. It also contains tools for the detection of secondary structure elements in macromolecular electron-density maps.

• RedMD   Molecular Dynamics

  GPL, (C, C++)

  • RedMD (Reduced Molecular Dynamics) is an open source package for molecular dynamics simulations and normal mode analysis for coarse-grained models of proteins and nucleic acids. Force fields are based on one-bead elastic network models and their extensions. The code is written in C/C++ and is parallelized.

• RM1   Quantum Mechanics

  • RM1 (Recife Model 1) is a reparameterisation of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. It is distributed as an external file for recent versions of MOPAC, as the default model for a modified version of the public domain MOPAC, and also can be implemented in HyperChem.

• RnaViz   3D Viewer

  GPL, (C, Tcl)

  • RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.

• SCHAKAL   3D Viewer

  Public Domain, Fortran

  • SCHAKAL is a FORTRAN program for the graphical representation of molecular and solid-state models.

• SCORE   Docking

  • SCORE is an empirical method for estimating the binding affinity of a protein-ligand complex with known 3D structure. SCORE uses a linear equation to describe the binding energy changes upon the binding process, which includes terms accounting for hydrogen-bonding, hydrophobic effect, and deformation effect.

• SHELX   Crystallography

  • SHELX is a set of programs for crystal structure determination from single-crystal diffraction data.

• SHELX-to-ORTEP   Crystallography

  • SHELX-to-ORTEP converts SHELX output files to ORTEP format.

• Siam Quantum

  GPL, C

  • Siam Quantum is an ab initio quantum chemistry program that uses quantum mechanics to determine the total energy and wave function of molecules within the framework of the Hartee-Fock method. The source code and documentation was originally designed to introduce students to electronic structure calculations. It can perform geometry optimisation and simple population analysis. Further developments are ongoing.

• SIMPSON   NMR

  GPL, C

  • SIMPSON is a General Simulation Program for Solid-State NMR. It features multi-pulse 1D/2D experiments on large spin-systems with input-files implemented using a simple scripting language. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, rf irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition.

• SIMREF   Crystallography

  • simref is a structure refinement program for the simultaneous evaluation of several powder diffraction data sets and multiple phases per data set. With a structural model all calculated diffraction profiles are fitted to the corresponding observed diffraction profile by the method of least squares. This procedure is called Rietveld method (Rietveld, 1969 ). By the simultaneous refinement of several data sets new evaluation techniques are possible.

• SimSoup   Reactions

  GPL, C++

  • SimSoup is is a graphical artificial chemistry simulator. The program enables a chemistry to be defined in terms of molecule types and the possible interactions between them. A simulation run involves setting up a number of molecules of various molecule types in a reactor, and then allowing interactions to take place over a period of time.

• Simulaid   Molecular Dynamics

  • Simulaid is a set of utilities to prepare molecular dynamics simulations. It features optimal solute placement, conversions between file formats and analysis of results.

• SIRware   Crystallography

  • The SIRware suite includes SIR97 (Direct Method program for the resolution and refinement of crystal structures using single crystal data), SIR2002 (Direct Method program for the resolution of proteins using single crystal data; can be used also for resolution and refinement of small and medium size crystal structures) and SIR2004 (automatic solution of crystal structures by Direct and Patterson Methods; it can be used both for resolution and refinement of small/medium size crystal structures and for macromolecules with data up to 1.4-1.5 Ang.)

• Situs   Crystallography, 3D Viewer, Docking

  GPL, C

  • Situs is an award-winning program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering. The software supports both rigid-body and flexible docking using a variety of fitting strategies.

• SketchEl   2D Draw

  GPL, Java

  • SketchEl is an interactive chemical molecule sketching tool, designed for quick and simple entry of structures. The feature set is limited to those necessary to enter a single chemical species, in a form that might be used in a cheminformatic database, representing each atom and bond as a part of a labelled graph.

• SnB   Crystallography

  • SnB is a program based on the Shake-and-Bake algorithm, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data.

• SNF   Quantum Mechanics

  GPL, (Fortran, C)

  • SNF has been developed for the calculation of Infrared, Raman, and VROA spectra using the harmonic approximation for the frequencies and the double harmonic approximation for the intensities. Vibrational frequencies are determined using numerical differentiation of analytical gradients of the total electronic energy, while infrared, Raman, and VROA intensities are obtained by numerical differentiation of dipole moments and (generalized) polarizability tensor components with respect to nuclear coordinates. Single point calculations are carried out using ADF, Dalton, Gaussian, Molpro or Turbomole.

• SODIUM   Molecular Dynamics

  • SODIUM can be used to arrange ions around biological macromolecules.

• Sparkle/AM1   Quantum Mechanics

  • Sparkle/AM1 is a computational chemistry model which exploits the lanthanide series characteristics to accurately predict geometries of the coordination polyhedra of complexes of ions of the rare earth metals. It is distributed as an external file for MOPAC 93r2, and as the default model for a modified version of the public domain MOPAC 6.

• Sparky   NMR

  • Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

• Spartan   Quantum Mechanics

  • Spartan is Wavefunction's flagship modeling software. It combines the versatility of Wavefunction's famous user interface and the power of Q-Chem's computational tools. It can carry out molecular mechanics, semi-empirical, ab initio Hartree Fock, DFT, Moller-Plesset, advanced correlated and excited state calculations. Available as a server or as a workstation edition.

• SPIN   NMR

  • SPIN calculates NMR spectra for systems of up to 9 spin 1/2 nuclei, given chemical shifts and coupling constants as inputs.

• spock   3D Viewer

  • Spock is a molecular visualisation program which can display and manipulate atoms, bonds, hydrogen bonds, solid and surfaces, CA traces, electrostatic potential contours, backbone worms, and even electron density maps. Spock can also be used for real-time conferencing over the internet. Spock is free for use in academic courses and for academics without sufficient funding.

• SPROUT   Cheminformatics

  • SPROUT is a de-novo ligand design system for developing novel active lead compounds. SynSPROUT uses synthetic rules to join fragments, and SPROUT-LeadOpt is designed for lead optimization.

• SSIA   NMR

  • SSIA is a program for predicting the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein or DNA/RNA) three-dimensional shape.

• Steric

  GPL Compatible, C

  • Steric calculates the steric size of molecules about a point in terms of their cone angles and solid angles, as well as their total volumes and projected areas.

• Swiss-PdbViewer   3D Viewer

  • Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

• Symmetry   Symmetry

  GPL, C

  • Symmetry is a set of C codes for automatic molecular symmetry recognition. Nothing fancy, but can be of use as an analytical or educational tool.

• Tessel   3D Viewer

  GPL Compatible, Fortran

  • Tessel2 is a 3D compiler to produce crystal and molecular models, parametric surfaces and several forms of sphere tesselations. The program produces output to be rendered with POV-Ray 2 or 3, Geomview (OFF format), or any Virtual Reality renderer (VRML V1.0 format).

• Thermo-Calc   Thermodynamics

  • Powerful and flexible software for all kinds of thermodynamic calculations in multicomponent systems. It is widely used to calculate phase diagrams, thermochemical data, solidification simulations and Pourbaix diagrams.

• Tinker   Molecular Dynamics

  • Tinker is a complete and general package for MM/MD, with some special features for polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER, CHARMM, MM2, MM3, OPLS, and our own AMOEBA force field based upon polarizable atomic multipole electrostatics.

• Triton   Quantum Mechanics, Protein reactions

  • Triton is a graphical tool for modelling protein mutants (using the external program MODELLER) and assessment of their activities (using the external program MOPAC). Semi-quantitative predictions of mutants' activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of the active site residues during the reaction.

• Turbomole   Quantum Mechanics

  • TURBOMOLE is a program package for ab initio electronic structure calculations. Outstanding features of TURBOMOLE are: semi-direct algorithms with adjustable main memory and disk space requirements; full use of all point groups; efficient integral evaluation; stable and accurate grids for numerical integration.

• "Understanding Molecular Simulations"   Molecular Dynamics

  • The FORTRAN source code of the Case Studies of the book Understanding Molecular Simulations.

• VAMP   Quantum Mechanics

  • Semiempirical program package containingthe MINDO3, MNDO, MNDOC, AM1 and PM3 Hamiltonian. It is capable of performing geometry optimisations as well as transition state searches and provides some extended multi center charge models (NAO-PC, HO-PC, LMO-PC); additionally, it may be used for some QM/MM calculations.

• VASP   Quantum Mechanics, Molecular Dynamics

  • Package for performing ab-initio quantum-mechanical MD using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.

• VASP Data Viewer   3D Viewer, Quantum Mechanics

  GPL, C

  • VASP Data Viewer is a visualization program for examining output files generated by the quantum chemistry package VASP.

• VB2000   Quantum Mechanics

  • VB2000 is an ab initio electronic structure package for performing modern Valence Bond (VB) calculations based on a highly efficient VB algorithm - the so called Algebrant Algorithm. It has also a general implementation of the Group Function (GF) Theory, in which a large molecule is described in terms of its constituent parts of physically identifiable "electron groups". It can be used as a stand-alone program, or as a plug-in module for GAMESS and Gaussian.

• VEGA   3D Viewer, Quantum Mechanics, Molecular Dynamics

  GPL Compatible, C

  • VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules.

• Vibrate   3D Viewer, Quantum Mechanics

  • Vibrate is a program for visualizing the normal vibrational modes of a molecule. Vibrate can read files generated by Mopac, Gaussian (G92 and G94), and HONDO and display the computed vibrational spectrum.

• Viewmol   3D Viewer, Quantum Mechanics

  GPL, (C, Python)

  • Viewmol is an open source graphical front end for computational chemistry programs. It can be used to build molecules, trace a geometry optimisation or MD trajectory, show vibrations, draw IR or Raman spectra, MO energy diagrams, and much more.

• VMD   3D Viewer, Molecular Dynamics, Quantum Mechanics

  • VMD is a program for visualization and analysis of the results of computational chemistry and molecular dynamics calculations. It can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.

• VolSurf   Cheminformatics

  • VolSurf is a computational procedure to produce 2D molecular descriptors from 3D molecular interaction energy grid maps. The basic idea of VolSurf is to compress the information present in 3D maps into a few 2D numerical descriptors which are very simple to understand and to interpret.

• Wat2ions   Molecular Dynamics, Utility

  • Wat2ions uses the electrostatic potential map pre-computed by DelPhi to replace a certain number of the water molecules of the bath, surrounding a solvated macromolecule, with ions. The new coordinates are output to a PDB file.

• WebMO   Quantum Mechanics, 3D Viewer

  • WebMO is a WWW-based interface to Gamess, Gausssian, Molpro, Mopac, Nwchem, Qchem, and Tinker for setting up, submitting, and visualizing results of computational chemistry jobs.

• WebMol   3D Viewer

  • WebMol is a Java-based PDB Viewer which can run as an applet in a web browser.

• WHAT IF   3D Viewer, Molecular Dynamics, Crystallography

  • WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, displaying the results of GROMACS calculations, analyse electron density maps, and much more.

• WIEN2k   Quantum Mechanics

  • WIEN2k allows the user to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one of the most accurate schemes for band structure calculations.

• WODCA   Reactions

  • WODCA (World of Computer Assisted Synthesis Planning or Workbench for the Organization of Data for Chemical Applications) is a computer program for the interactive planning of organic syntheses, in particular, for the planning of organic syntheses in a retrosynthetic approach. Built-in catalogs of fine chemicals like those from Acros Organics or Fluka Chemical Company provide suitable starting materials for a synthesis target.

• XChemEdit   3D Viewer, Quantum Mechanics

  • XChemEdit is a package of programs which can draw and edit three-dimensional chemical structures; serve as a graphical interface to the GAUSSIAN, JAGUAR, MOPAC, and BOSS/MCPRO programs; display molecular orbitals, electron densities, and electrostatic potentials; animate normal mode vibrations; and compute solvent-accessible surface area, volume, and thermochemical properties.

• XCombust   Utility

  • Who in chemistry never experienced the following: You get your sample back from the analytical department and look shyly at the elemental analysis data - and they are way off. So what usually happens is that one tries to make the numbers fit by postulating solvent inclusion (like 1 mol of EtOH) and then get stressed out with a desktop calculator. That's where this tiny shiny utility comes into play.

• XCrySDen   3D Viewer, Crystallography

  GPL, (Fortran, C)

  • XCrySDens (Crystalline Structures and Density) is a crystalline and molecular structure visualisation program, which can superimpose isosurfaces and contours onto crystalline structures and interactively rotate and manipulate them. XCrySDens also provides a (partial) graphical user interface for CRYSTAL, and a visualisation system for PWscf and WIEN2k.

• XDrawChem   2D Draw

  GPL, (Fortran, C++)

  • XDrawChem is 2D molecule drawing program. Some notable features include the ability to retrieve structures from a network database given the name or CAS number; it can predict predict proton and C13 NMR shifts; and it can interface with OpenBabel to read and write multiple file formats.

• XEASY   NMR

  • XEASY is a program to display and assign 2D, 3D, and 4D NMR spectra.

• xem   Education

  GPL, C++

  • xem is a simple software simulating titration for various systems.

• XLOGP/PLOGP   Cheminformatics

  • Method which can calculate the logP value for an organic compound from its topological structure. The algorithm is based on the summation of atomic contributions and correction factors.

• XMakemol   3D Viewer

  GPL, C++

  • XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

• XMD   Molecular Dynamics

  GPL, C

  • XMD performs Computer Molecular Dynamics (CMD) simulations on metals and ceramics.

• XmMol   3D Viewer

  GPL, C

  • XmMol is a desktop macromolecular visualization and modeling tool designed to be easy to use, configure and enhance. Its graphics are based on X11, and part of its user interface is based on Motif. Thus it provides a way of displaying structures on any X11 server.

• XMolCalc   Utility

  • XMolCalc is a small utility that allows you to calculate a molecular weight under Unix/X11.

• XNMR   NMR

  • XNMR is an X11 based program capable of simulating exchange broadened NMR spectra of dynamic molecules with up to nine chemical configurations. XNMR further supports up to a certain degree the processing of experimental data obtained from Bruker NMR spectrometers running UXNMR or XWin-NMR.

• XOrtep   Crystallography

  • XOrtep is is a slightly modified version of the ortep-for-sun code that was written to provide an editor/previewer combination based on Sun's OpenView toolkit.

• XPMA   Crystallography

  • XPMA is a mouse driven menu based graphical program for the manipulation of crystal structures. It reads SHELX93, SHELXL, SHELX76 and SHELXS-OUTPUT FILES.

• XPovChem   3D Viewer

  GPL, C

  • XPovChem is a molecule viewer based on the PovRay raytracer. It takes a molecule description, converts it into a .pov file, and lets povray render the image -- thus allowing a very high rendering quality. Xpovchem includes the professional Babel molecule format converter and is a GUI frontend to Paul Thiessen's povchem console program.

• XRDL   Crystallography

  • XRDL is reciprocal space viewer written in Java. It is also released as part of JSV. It allows real-time rotation of the reciprocal lattice points. This software is 'Charityware'.

• X-UTIL   Crystallography

  • X-UTIL is a set of utility programs intended for (but not limited to) practising protein crystallographers.

• XVibs   3D Viewer, Quantum Mechanics

  GPL, Java

  • XVibs is a utility for animating molecular vibrations. Normal modes are read from a file automatically determined to be from Aces2, Gamess, PC Gamess, Gaussian 90/92/95/94/98, ADF, Dalton, Jaguar, MOPAC, or HyperChem. Separate animation files are written for each vibration.

• YAeHMOP   Quantum Mechanics

  GPL, (C, Fortran)

  • Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions.

• Yambo   Quantum Mechanics

  GPL, (C, Fortran)

  • Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by the DFT codes abinit and Pwscf.

• YASARA Dynamics   3D Viewer, Molecular Dynamics

  • YASARA Dynamics contains YASARA View and adds support for molecular simulations. Beside the YASARA NOVA Force Field and the new highly accurate YAMBER force fields, you can use other well known MD force fields like AMBER, and run accurate all-atom MD simulations in aqueous solution with Particle Mesh Ewald longrange electrostatics at twice the speed you know from other programs. YASARA Dynamics is not a black box with input and output files, but shows the MD simulation in real-time on screen. You can fully interact with the scene, pull atoms or whole molecules around.

• YASARA View   3D Viewer

  • Explore macromolecular structures interactively with YASARA View, whose innotive 3D engine is up to 35 times faster than OpenGL. You can load multiple structures at the same time, create publication-quality ray-traced images including labels, and program your own macros and Python plugins.

• YMOL   3D Viewer

  • Molecular visualisation and animation program, which can be used to create production quality images, and movies, using either the built in renderer or by exporting the scenes to POVRAY.

• ZMM   Molecular Mechanics

  • ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions of free molecules and ions, and orientation of free molecules.

• Zodiac

  GPL, C++

  • Zodiac is an advanced molecular editor for molecular modelling and computer aided drug design, that offers tools such as energy minimisation, database management, molecular property prediction and front ends to various docking and QM programs. It is cross platform and released under the GPL.

• ZORTEP   Crystallography

  • ZORTEP is a mouse driven, menu based graphical ORTEP program. This allows the 'real-time' graphical rotation and manipulation of structures and/or thermal ellipsoids on the screen.

323 results found