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Software

2D-Numerical  links

A numerical Hartree-Fock program for diatomic molecules.

Abinit  links

Abinit is a package whose main program allows to find the total energy, charge density and electronic structure of systems made of electons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a plane wave basis.

APBS  links

APBS (Adaptive Poisson-Boltzmann Solver) is a software for evaluating the electrostatic properties of nanoscale biomolecular.

ASAP  links

ASAP (As Soon As Possible) is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). ASAP currently implements the Effective Medium Potential (EMT) for the elements Ni, Cu, Pd, Ag, Pt and Au (and their alloys). There is also experimental support for Mg and Mo. It supports simulations on parallel clusters.

ASE  links

The Atomic Simulation Environment (ASE) is the common part of the simulation tools developped at CAMP. The ASE provides modules for moving atoms, analyzing simulations etc. The ASE is not able to calculate energies or forces on the atoms, for this task it relies on a number of Calculators. A calculator may do a complete quantum-mechanical calculation, or may use simpler (semi-)empirical potential.

Babel  links

Babel is a program to interconvert file formats used in molecular modeling.

Ballroom  links

BallRoom is a visualization tool for set of particles. It displays particles as balls (no sticks here), and uses a representation projected on two dimensions (no real 3D features like lights, shadows).

BigMAC  links

Configurational-Bias Monte Carlo of Linear Alkanes.

Bika  links

BIKA is a laboratory information management system (LIMS) built on top of Zope and Plone, and coded in Python.

Bioclipse  links

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).

BKchem  links

BKchem is a chemical drawing program written in Python.

Blue Obelisk Data Repository links

This project includes many important chemoinformatics data such as elemental properties, atomic radii, etc. including references to original literature.

CCP1GUI  links

The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes.

Checkmol/Matchmol  links

Checkmol is a command-line utility program which reads molecular structure files in different formats and analyzes the input molecule for the presence of various functional groups and structural elements. Matchmol complements the capabilities of checkmol. It compares two (or more) molecular structures and determines whether one of them is a substructure of the other one. This is done by a full atom-by-atom comparison of the input structures. Thus, matchmol can be used as a back-end program for structure/substructure search operations in chemical databases.

ChemCalc  links

A calculator that is more oriented towards chemistry.

ChemCpp links

ChemCpp is a C++ toolbox for chemoinformatics focusing on the computation of kernel functions between chemical compounds. Together with Support Vector Machines, these kernel functions find natural applications for virtual screening of molecules.

Chemeq  links

Translate chemical equations to LaTeX code.

Chemical Structures links

The Chemical Structures Project aims to provide a complete set of 3D molecular structures in CML format.

ChemicalInventory  links

ChemicalInventory is a chemical intelligent tool for managing chemical inventories. Main features: Find chemicals via substructure or text searches. Manage container and shelf locations, check containers in and out or transfer containers between users.

ChemNomParse  links

The ChemNomParse project is an open source project to create a chemical nomenclature parser. The project aims to build molecules from an IUPAC chemical name and comes in two parts: ChemNomParse and Nomen

Chemsuite  links

A Molecular 2D/3D drawing and chemical reaction simulation software.

Chemtool  links

Chemtool is a small program for drawing chemical structures on GNU/Linux and Unix systems using the GTK toolkit under X11.

CHIMP  links

CHIMP is a generic tool for the modeling of chemical phenomena. Eventually, chemical reaction modeling, molecular mechanics, and quantum mechanic modules will be implemented, along with an easy to use graphical user interface (GUI). At present, CHIMP has the ability to perform dynamic Monte Carlo simulations on chemical reactions, in particular heterogeneous catalytic reactions.

Coot  links

Coot is for model building, model completion and validation. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots...

CRK  links

The CRK (Chemical Resource Kit) is the collective name describing three chemistry-related software packages : Xykron (front end for a collection of tools for managing, manipulating and presenting chemical data), Xentark (The computational arm of CRK) and Xortoth.

Dacapo  links

Dacapo is a total energy program based on density functional theory. It uses a plane wave basis for the valence electronic states and describes the core-electron interactions with Vanderbilt ultrasoft pseudo-potentials.

DFT++  links

This software performs complex density functional calculations. It is fully cache and register optimized, and runs in serial, threaded, MPI and mixed threaded-MPI parallel environments.

DND  links

DND stands for Dream aNd Dreamer. The DND project intends to build a complete, user-friendly GUI of the Molecular Dynamics Simulation of the Molecule on free software.

EasyChem  links

EasyChem is a program designed to draw chemical molecules, written under Linux and using Gtk+ 2.

EChem++  links

EChem++ is a software system based on an object oriented approach to electrochemical experimentation, simulation, and data analysis. Currently, development emphasis lies on the modelling and simulation as well as the analysis modules.

EDEN  links

A crystallographic real-space electron-density refinement and optimization program.

EGO  links

EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX and inhomogeneous clusters of UNIX workstations under PVM or MPI.

Elem  links

Elem is a periodic table of the elements.

EMAN  links

EMAN is a set of image/volume processing tools to perform single particle reconstructions. This is a technique for determining the 3 dimensional structure of a molecule from thousands to hundreds of thousands of noisy images of individual molecules. There are other techniques for performing this task, such as x-ray diffraction, NMR spectroscopy, and 2d/helical electron crystallography.

Espoir  links

Espoir is a reverse Monte Carlo and pseudo simulated annealing code for ab initio crystal structure determination, either from scratch (random starting model) or by molecule location, fitting either to Fobs extracted by powder diffractometry or to single crystal data.

Fox  links

The FOX program (for Linux and Win32) was made for the ab initio crystal structure solution from diffraction data (mostly powder diffraction data).

Frowns  links

Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry related algorithms. It is written in almost 100% Python with a small portion written in C++.

Fungimol  links

Fungimol is an extensible system for designing atomic-scale objects. The intent is to eventually extend it to be a useful system for doing molecular nanotechnology design work.

Gabedit  links

Gabedit is a Graphical User Interface to Gaussian, Molcas, Molpro and MPQC computational chemistry packages. Gabedit includes graphical facilities for generating keywords and options, molecule specifications and ther input sections for even the most advanced calculation types

GAMGI  links

GAMGI is a free computer package to construct, view and analyse atomic structures, as powerful and simple to use as possible.

Garlic  links

Garlic is a free molecular visualization program written for unix and unix clones. Now, it is able to edit the molecule.

GChemPaint  links

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 some chemistry can be embedded in other Gnome applications. It can also be used to display chemical formula in Mozilla or derived browser with the help of mozilla-bonobo.

GChemUtils  links

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

GDIS  links

GDIS is a GTK based program for the display and manipulation of isolated molecules and periodic systems. It is in development, but is nonetheless fairly functional.

GDPC  links

GDPC is a program for visualising molecular dynamic 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.

GenChemLab  links

GenChemLab is an OpenGL-based application intended to simulate several common general chemistry exercises. It is meant to be used to help students prepare for actual lab experience. It could also be used in cases where laboratory facilites are not accessible, for instance in K-12 schools or home schooling.

Ghemical  links

A molecular modelling software package with nice 3D-visualization tools.

GLARE links

GLARE is a software that facilitates and improves the design of chemical combinatorial libraries.

Gnome Crystal links

Gnome Crystal (also called GCrystal) should display models of all sorts of crystal microscopic structures using OpenGL. It can be used as a Bonobo server to embed the display in other Gnome applications.

GNU/PolyXmass  links

This program is a framework for doing mass spectrometric data analysis/prediction on a variety of polymers.

gOpenMol  links

gOpenMol is a tool for the visualization and analysis of molecular structures.

GPeriodic  links

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

GRINSP  links

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

Gromacs  links

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

IPC  links

IPC (Isotopic Pattern Calculator) is a program that calculates the isotopic distribution of a given chemical formula. It gives the rel. intensities and the propability of the masses belonging to a molecule ion, fragment or whatever is represented by the given chemical formula. Furthernmore it can use GNUPlot to visualize the result. A GUI is also available (GIPS).

JChemPaint  links

JChemPaint is an editor for 2D Molecular Structures. JChemPaint is intended to be complementary to JMol, a visualization and analysis tool for 3D molecular structures, started by Dan Gezelter at Notre Dame University, initator of the Open Science Project and, like JChemPaint, developed by an international team of open-source programmers.

Jmol  links

Jmol is a Free, Free Software molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.

JOELib  links

JOELib is a computational chemistry library which supports SMARTS substructure search, descriptorcalculation, processing/filtering pipes, conversion of different chemical file formats ... 100% pure Java ... and interfaces to external programs are available

Kalzium  links

Kalzium is an application which will show you some information about the periodic system of the elements.

Kci  links

Kci transforms chemical equations into simulation programs.

Kemistry  links

Kemistry is a collection of chemistry-related applications for KDE.

KMol  links

KMol is a molecular weight and elemental composition calculator.

KMovisto  links

KMovisto is a molecule viewer for using in quantum chemistry. The program reads GAUSSIAN 94 and GAUSSIAN 98 files (obtained from UNIX or MS Win32 systems) or XYZ files and draws the molecule as a ball and stick model.

KOpenBabel links

KOpenBabel is a graphical interface to Open Babel. Two versions of this software are available (KDE and Qt).

LAMMPS  links

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. It's a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, or granular systems using a variety of force fields and boundary conditions.

Lennard  links

Nobel Gas Simulator.

LSD  links

The aim of the LSD program is to find all possible molecular structures of an organic compound that are compatible with its spectroscopic data. Structure building relies on connectivity data found in 2D NMR spectra, without any reference to a chemical shift database. Molecular structures containing up to 50 non-hydrogen atoms were investigated by means of the LSD program.

Maxit  links

Maxit is an application for processing and curation of macromolecular structure data.

MCCCS Towhee links

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.

McMaille  links

McMaille is a program for indexing powder patterns by Monte Carlo and grid search (maille in french = cell in english).

MMTK  links

The Molecular Modelling Toolkit (MMTK) is an Free Software program library for molecular simulation applications.

MOIL  links

MOIL is a molecular modeling software written in the group of Ron Elber. In addition to widely available features, such as energy calculations, minimization and calculations of classical trajectories, MOIL has a few special features that are difficult to find in general modeling packages, like Locally Enhanced Sampling (LES), long time dynamics algorithms or a Landau-Zerner model to dissociation and recombination of ligands, and curve crossing.

Moldy  links

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. The system is specified at run time with a description file so there is no need to recompile when changing systems. The program handles much more of the bookkeeping than is traditionally done, keeping track of consistency of parameters, restart files, output trajectories and so forth. Sizing of arrays limits are all handled automatically.

Molekel links

Molekel is a multiplatform molecular visualization program.

MOPAC7  links

MOPAC7 is an autotooled, updated version of a powerful, fast semi-empirical package.

MOSCITO  links

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.

MPQC  links

MPQC is the Massively Parallel Quantum Chemistry Program.

MWCalc links

A simple but powerful molecular weight calculator.

NanoCAD  links

NanoCAD uses mathematical techniques of molecular modeling to simulate the behavior of molecules on your web browser.

nMOLDYN  links

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.

ObjCryst++  links

The aim of this project is to provide object-oriented tools for Crystallography. The focus of these tools is the analysis of diffraction data, with an emphasis on speed optimization for repetitive calculations (for global refinement methods such as simulated annealing, for example).

Octet  links

Octet is a new system of lightweight and interoperable molecular informatics components written in Java. Octet's goal is to simplify the development of platform-independent molecular informatics applications.

OpenBabel  links

OpenBabel is a project designed to pick up Babel left off, as a cross-plateform programm and library designed to interconvert between many file formats used in molecular modelling ans computanional chemistry.

OptiCat links

OptiCat is a platform for building stochastic optimization algorithms.

ORAC  links

ORAC is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles.

OSET  links

Computer-Assisted Organic Synthesis (CAOS) program for use in the teaching of Organic Chemistry, and retrosynthetic analysis in particular.

PDB-extract  links

The Pdb Extract Program Suite contains tools and examples for extracting mmCIF data from structure determination applications.

PerlMol  links

PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that simple things should be simple. It should be possible to write one-liners that use this toolkit to do meaningful molecular munging.

PEtot  links

PEtot stands for parallel total Energy (Etot). It is a parallel plane wave pseudopotential program for atomistic total energy calculation based on density functional theory. It is designed for large system simulations to be run on large parallel computers like IBM SP machines at NERSC, and linux cluster machines.

PINY_MD  links

PINY_MD(c) is a multipurpose, object-oriented molecular simulation package. PINY_MD(c) is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations. Such capabilities include force-field based (``classical'') simulations on system ranging in complexity from simple molecular liquids (.e.g, water, ammonia, liquid alkanes) and crystals (e.g., ice) to large biomolecular systems such as the HIV-1 protease in solution.

ProtoFit  links

ProtoFit is a tool for optimization of surface protonation models from acid-base titration data. The software consists of two parts: ProtoFit, which is the program for model parameter optimization and simulation; and ProtoFit-GUI, a graphical user interface to ProtoFit with data and model visualization capabilities. ProtoFit-GUI provides for easy simulation of titrations and graphical comparison of model with measurements.

PSI3 links

The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules.

PWscf  links

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.

PyMOL  links

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.

PyMOlyze  links

PyMOlyze is a program to analyze the results of quantum chemistry (DFT) calculations. Gaussian 03, ADF and Jaguar 6.0 files are supported.

RasMol  links

RasMol (or OpenRasMol) is a software for molecular structure visualization.

RasTop  links

RasTop is a molecular visualization software adapted from the program RasMol.

SCHAKAL 99  links

SCHAKAL 99 is a computer program for the graphic representation of molecular and solid-state structure models.

ScreeningAssistant  links

ScreeningAssistant is a software based on JOELib and dedicated to the management of chemical databases. It allows the user to select a set of compounds for screening tests (High Throughput Screening or Virtual Screening).

Situs  links

Situs is a 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.

Spinor  links

The ab initio Spinor Project is a scientific code project based on density functional theory (DFT) within the ab initio pseudopotential framework. The code implements the fundamental Kohn-Sham functions in form of two-component spinors.

Structure  links

Structure is a framework for two-dimensional molecular visualization written in Java and based on Octet.

Taverna  links

The Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community.

Tigress  links

Tigress is a chemoinformatics extension to the PostgreSQL DBMS. It enables PostgreSQL to store, retrieve and search chemical datatypes, i.e. Molecules for the time being, by pure SQL statements. It uses checkmol/matchmol and OpenBabel.

Validation  links

Validation is a set of tools used by the PDB for processing and checking structure data.

VASP Viewer  links

This is a scientific visualization package for examining output files generated by the Vienna Ab-initio Simulation Package, a package for performing ab-initio quantum-mechanical molecular dynamics using pseudopotentials and a plane wave basis set.

Viewmol  links

Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

Volta links

Volta is a small Python program that drive a PARC 273 potentiostat.

XDrawChem  links

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications. XDrawChem has been tested on GNU/Linux, SGI IRIX 6.5, and Sun Solaris.

Xem  links

This software can draw quickly acid/base titration diagramme

XMakeMol  links

XMakemol is a program written for UN*X operating systems in ANSI C using the X, Xt and Motif libraries. It can be use to view and manipulate atomic and molecular data given in xyz format.

xyz2rgb  links

xyz2rgb makes pretty pictures and movies of molecules. It expects input in the form of an XYZ file, one of the file formats frequently used by computational chemists. As output, it produces one or more line-interlaced RGB files.

YAeHMOP  links

A package of programs for performing extended Hueckel calculations on molecules and solids and visualizing the results. Visualization functionality for some quantum packages (ADF and LMTO) is also provided.

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Software News

Mychem 0.7.0 released

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Bioclipse 2.0 released

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Open Babel 2.2.2 released

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Open Babel 2.2.1 released

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Mychem v0.6.0 Released

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