Chemistry, Biology & Related software for Linux  
( Commercial,  Shareware,  GPL)
[Linux: home, news, download]

ABaCUS -- investigate the significance of the putative correspondence between exons and units of protein structure.
Acedb -- a genome database system.
AMBER -- simulation of biomolecules and molecular simulation programs.
Angler -- a browser application for exploring C.elegans embryo development data in time and space.
ASAD -- a package for integrating chemical schemes in atmospheric models.
AutoDock -- automated docking of flexible ligands to macromolecules.
autoseq -- a small package of base calling software for ABI automated DNA sequencers.
Babel -- interconverts a number of file formats currently used in molecular modeling.
BIGMAC -- a recent technique to compute thermodynamic properties of flexible molecules.
Biomer -- a web-based molecular modeling package for small organic molecules.
Biostatistics Software -- collection of software for biostatistics research.
BLAST -- a sequence similarity search tool supporting analysis of nucleotide and protein databases.
BOSS -- biochemical and organic simulation system.
BRAGI -- an interactive protein-modelling program.
BTL -- a bioinformatics template C++ library.
CACTVS Tools -- A visualization package for chemist.
ChemApp -- a programmable thermodynamic calculation interface.
ChemSymphony -- a set of interactive Java applets for 3-D molecular structures in WWW.
Chemtool -- drawing organic molecules easily and store them as a X-Bitmap file.
CloneIt -- finding sub-cloing strategies, in-frame deletions, and frameshifts strategies.
ClustalW -- multiple alignments of DNA or protein sequences.
Cn3D -- a molecular structure viewer that is based on the Entrez data model.
COLUMBUS -- high-level ab initio molecular electronic structure calculations.
CRYSTAL -- computes electronic structure of periodic materials with quantum mechanical methods.
Dalton -- a quantum chemistry program for molecular properties.
DBWatcher -- a program handling periodic BLAST searches to find similarities to your own sequences.
DCSE -- a multiple alignment editor for protein, DNA or RNA alignments.
DeFT -- a quantum mechanical and Gaussian density functional program.
Democritos -- a set of C++ classes with support for bioinformatics and computational chemistry.
DL_POLY -- a parallel molecular dynamics simulation package.
DND -- intend to build a GUI for molecular dynamics simulation of molecule.
DOCK -- a program for matching molecules to potential binding sites on macromolecules.
DomainFinder -- identifies and characterizes dynamical domains in proteins.
Dotter -- a dot-matrix program with greyscale rendering for genomic DNA and Protein sequence analysis.
Dynamite -- a code generating language developed for sequence comparison methods.
EGO -- molecular dynamics calculations on parallel/sequential computers.
EMBOSS -- suite of programs and libraries for sequence analysis.
Evalign -- a computerised evaluation method for protein sequence alignment algorithm.
FANTOM -- fast newton-raphson torsion angle minimizer.
Fasta -- biological sequence analysis including programs for library search, local homology.
fastDNAml -- construction of phylogenetic trees of DNA sequences.
fetch -- swissprot protein sequence retrieval utility.
G_neuron -- a single neuron simulator for Hoggkin-Huxley model.
GAMESS -- quantum chemistry.
GAMMA -- construction of programs that simulate magnetic resonance phenomena.
Gaussian -- an electronic structure program for chemists.
GEANFAMMER -- GEnome ANalysis and Protein FAMily MakER.
GeneMark -- a package for finding gene locations within unannotated sequence texts.
GeneMine -- bioinformatics data mineing and data visualization.
GERM -- genetically evolved receptor models.
GIFA -- processing, the visualization and the analysis of 1D, 2D, and 3D NMR data-set.
gOpenMol -- graphics interface to the OpenMol set of programs.
GPeriodic -- a periodic table reference software.
GROMACS -- a set of molecular dynamics code and analysis tools for parallel computers.
GROMOS -- a general-purpose molecular dynamics simulation package for biomolecular systems.
GRS -- a graphic tool for genome retrieval and segment analysis.
HMMER -- large-scale genome analysis using probabilistic models of proteins and RNAs.
ICM -- molecular modeling; molecular visualization and animation;
ICMLite -- a great new free molecular graphics program.
Jaguar -- an extremely fast ab initio electronic structure software package.
kc -- transforms chemical equations into simulation programs.
KMol -- a molecular weight and elemental composition calculator.
LASSAP -- an extensible, high performance , parallel sequence comparison software.
Lennard-Jones Gas Simulation -- using molecular dynamics.
Mage -- a browser called for kinemage file format.
MEXICO -- a program for calculating lineshapes in the NMR spectrum of exchanging species.
MidasPlus -- an advanced molecular display and simulation system.
Molecular Modeling Toolkit -- a library for molecular modeling.
MODELLER -- a program for homology protein structure modelling by satisfaction of spatial restraints.
MOISS -- a n-particle, n-dimensions Monte Carlo Schroedinger equation integrator.
Molden -- a pre- and post processing program of molecular and electronic structure.
MOLCAS -- a quantum chemistry software for molecular systems.
Moldy -- performs molecular dynamics simulations of condensed matter.
MOLPHY -- a program package for MOLecular PHYlogenetics.
MOLMOL -- molecular graphics program for displaying, analyzing, and manipulating the 3D structure.
MOLPRO -- a complete system of ab initio programs for molecular electronic structure calculations.
MOLSCAT -- quantum mechanical solution of the nonreactive molecular scattering problem.
MolScript -- a program for displaying molecular 3D structures.
MOPAC -- general-purpose semi-empirical molecular orbital package.
MPQC -- massively parallel quantum chemistry program.
NAMD -- parallel, object-oriented molecular dynamics program.
NanoCAD -- a CAD system for Nanotechnology.
Naccess -- calculates the accessible area of a molecule from a PDB file.
NCBI Toolkit -- a library for developing biology programs.
NJplot -- a tree drawing program for any binary tree expressed in the standard phylogenetic tree format.
NWChem -- high performance computational chemistry software.
ORAC -- a molecular dynamics program to simulate solvated biomolecules.
ORTEP-III -- drawing crystal structure illustrations.
PADRE -- population analysis and duplicate removal.
PALLAS -- software predicting pKa,logP, logD values and metabolites.
PAML -- phylogenetic analyses of DNA or protein sequences using maximum likelihood.
PEST -- software for the acquisition and analysis of EPR data.
PHYLIP -- a package of programs for inferring phylogenies.
PHYLO_WIN -- a graphic tool for molecular phylogenetic inferences.
PIMM -- combined SCF/molecular mechanics program for organic molecules and complexes.
PLATON -- versatile crystallographic tool.
Pluton -- interactive molecular graphics.
PMD -- a scalable, parallel program for the simulation of biological macromolecules.
POLYRATE -- calculation of chemical reaction rates of polyatomic species.
PomBase -- database merges the genomic sequence data with maps, genetics and bibliography.
Protein Structure Software -- programs and C libraries.
PovChem -- generates POV-Ray files from Protein Data Bank.
PROCHECK -- programs to check the stereochemical quality of protein structures.
PUZZLE -- reconstructs phylogenetic trees from molecular sequence data by maximum likelihood.
Q-Chem -- an ab initio quantum chemistry software product.
QCPE LINUX Software Program -- several quantum chemistry programs.
RasMol -- molecular graphics program intended for the visualisation.
RASSE -- a structrue-based method for de novo drug design.
Raster3D -- set of tools for generating high quality raster images of proteins or other molecules.
RdLength -- calculates the Radiation Length of a single molecule based on its empirical formula.
The Remote Microscope -- remotely controllable optical microscope over the Internet.
RnaViz -- a friendly/portable program for producing secondary structure drawings of RNA molecules.
SC_rate -- produces position specific reliability prediction for any protein sequence alignment.
SCWRL -- a program for adding sidechains to a protein backbone.
SEALS -- a system for easy analysis of lots of sequences.
SeqPup -- a biological sequence editor and analysis program.
Sequin -- a DNA sequence submission and update tool.
SIMPLTN -- simulation of pulse and two-dimensional NMR.
SIR92 -- automatic solution of crystal structures by direct methods.
SOLVATE -- construct an atomic solvent environment model for MD simulation.
Spock -- a full-featured molecular graphics program.
steric -- a program for the calculation of molecular steric parameters.
TheRate -- an intuitive teaching tool for courses in applied quantum chemistry and kinetics.
Thermo-Calc -- a software package for thermodynamics equilibrium and phase diagram calculations.
TINKER -- a package for molecular mechanics and dynamics of molecules, especially polypeptides.
tacg -- command line tool for the restriction enzyme analysis of DNA.
TULIP -- project to develop a software for DNA and protein analyses.
Turbo Frodo and Turbo X -- a general purpose molecular modelling environnement.
TURBOMOLE -- a package for ab initio electronic structure calculations.
Understanding Molecular Simulations -- software for Molecular Simulation.
VASP -- ab-initio MD simulation with pseudopotential and plane wave basis set.
viewmol -- a GUI for some quantum chemical and some molecular modelling programs.
VMD -- a molecular visualization and analysis program.
Weber's Java codes -- various Java codes for visualization in crystallography area.
WHAT IF -- a versatile protein structure analysis program.
WIEN97 -- perform electronic structure calculations of solids using LAPW method.
Wise2 -- comparing DNA sequences at the level of its conceptual translation.
WWWtacg -- web interface to tacg.
XBS -- a simple but useful program for plotting ball-and-sticks models of molecules or crystals.
XEASY -- NMR spectrum analysis.
xelem -- displays a hypertext periodic table with many information.
XEMR -- a software package written for electron magnetic resonance (EMR) spectroscopists.
XNBC -- simulating biological neural networks.
XNMR -- a program for processing NMR spectra.
X-PLOR -- computational structural biology, X-ray crystallography and NMR.
XtalView -- solving a macromolecular crystal structure by isomorphous replacement.
xyz2rgb -- a tool for animating molecules.

Linux and Chemistry : Links to chemistry software on Linux.

Steven's List of Chemistry Software for Linux/UNIX

Molecular Bilogoly related programs for Linux. Including many software and binaries compiled on Linux.

Molecular biology, biochemistry applications under Linux

Biocomputing and Linux

Software for Biology

CSIR (Chemistry Software and Information Resources) is an information resource for chemistry software, its development, and its use (in the broadest sense). It brings together a great deal of information scattered across the Internet, often hard to find and use, and makes it easily available to anyone with a web browser.

MD Anderson Cancer Center -- Biomathematics Archive: contains computer code written by members of the Department of Biomathematics, the University of Texas M. D. Anderson Cancer Center. The code can be freely copied and used (shareware distribution is encouraged) although the authors retain copyright for the University of Texas in order to control possible commercial incorporation. The last section of this message contains instructions on how to obtain it.

Computational Chemistry List (CCL) -- an independent electronic discussion forum for chemistry researchers and educators from around the world. It includes CCL archives, which contain archived messages, software, documents, data, and information related to computational chemistry.

Compilation of Educational NMR Software

QCPE (Quantum Chemistry Program Exchange)

WWW Virtual Library: Chemistry
http://www.chem.ucla.edu/chempointers.html