SAL Home OTHERS Chemistry, Biology & Related

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Initially I was a bit puzzled to setup a section like this one, because there are already several nice web pages about this topic specifically for Linux (as seen in Other Resources below). But how can SAL live without some of these wonderful software? So I decided to put a fraction of the chemical/biological software here to give you an idea about how popular the Linux is used in this area.

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Chemistry, Biology & Related   ([CM] Commercial, [SR] Shareware, [GPL] GPL)

ABaCUS -- investigate the significance of the putative correspondence between exons and units of protein structure.
Acedb -- a genome database system.
ADF [CM] -- Amsterdam Density Functional program for computational chemistry research.
AMBER [CM] -- simulation of biomolecules and molecular simulation programs.
AMMP [GPL] -- a modern full-featured molecular mechanics, dynamics and modeling program.
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.
NEW BioJava [GPL] -- providing Java tools for processing biological data.
BioMail [GPL] -- retrieve latest information about a disease or biological phenomenon.
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 [GPL] -- a bioinformatics template C++ library.
CACTVS Tools -- A visualization package for chemist.
CDA -- analyze chemical systems which can be described as donor-acceptor complexes.
ChemApp -- a programmable thermodynamic calculation interface.
ChemCalc [GPL] -- a calculator that is more oriented towards chemistry.
chemeq [GPL] -- translate chemical equations to LaTeX code.
ChemSol -- calculates solvation free energies with Langevin Dipoles solvation model.
Chemsuite [GPL] -- molecular 2/3D drawing and chemical reaction simulation software.
ChemSymphony [CM] -- 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.
NEW Chime -- a web browser plugin for displaying 3D molecular structure.
CHIMP [GPL] -- a generic tool for the modeling of chemical phenomena.
Clarrhmos [GPL] -- a clinical arrhythmia model simulator.
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.
NEW Chemical Resource Kit [GPL] -- includes three chemistry-related software packages.
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.
DINO -- a visualization program for structural biology data.
DL_POLY -- a parallel molecular dynamics simulation package.
NEW DNA/GUI -- GUI for quantitative imaging and analysis of electrophoretic gels and autoradiograms.
DND [GPL] -- 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 [GPL] -- a code generating language developed for sequence comparison methods.
E-Cell -- a modeling and simulation environment for biochemical and genetic processes.
EGO -- molecular dynamics calculations on parallel/sequential computers.
EMBOSS [GPL] -- 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 [GPL] -- construction of programs that simulate magnetic resonance phenomena.
Garlic [GPL] -- a free/open source molecular visualization program for UNIX/Linux.
Gaussian [CM] -- an electronic structure program for chemists.
gBioSeq -- a graphical multiple DNA sequence alignment editor.
NEW GDE -- a set of programs for multiple sequence alignment and analysis.
NEW gdis [GPL] -- a GTK based program for visualizing molecules and periodic systems.
gdpc [GPL] -- a program for visualising molecular dynamic simulations.
GEANFAMMER -- GEnome ANalysis and Protein FAMily MakER.
GeneMark [CM] -- a package for finding gene locations within unannotated sequence texts.
GeneMine [CM] -- bioinformatics data mineing and data visualization.
Genpak [GPL] -- a set of small utilities to manipulate DNA sequences in a Unix fashion.
NEW GENSPECT -- spectral toolbox for calculating spectral properties of gases.
GERM [CM] -- genetically evolved receptor models.
Ghemical [GPL] -- a molecular modelling software package with nice 3D-visualization tools.
GIFA -- processing, the visualization and the analysis of 1D, 2D, and 3D NMR data-set.
gOpenMol -- graphics interface to the OpenMol set of programs.
NEW GP/Arka [GPL] -- a set of small utilities to manipulate DNA sequences and a GUI program.
GPeriodic [GPL] -- 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.
NEW GtkChemkin [GPL] -- handles save-files written by the chemkin program.
NEW GULP -- simulation on 3D periodic solids, gas phase clusters and isolated defects in a bulk material.
HMMER [GPL] -- large-scale genome analysis using probabilistic models of proteins and RNAs.
ICM [CM] -- molecular modeling; molecular visualization and animation;
ICMLite -- a great new free molecular graphics program.
Jaguar [CM] -- an extremely fast ab initio electronic structure software package.
NEW JChem -- a development tool in Java for manipulating mixed chemical and corporate data.
JChemPaint [GPL] -- a program for drawing 2D chemical structures, written in Java.
JCFL [GPL] -- Java library for utilizing Chemical Markup Language (CML).
Jmol [GPL] -- an open-source molecule viewer and editor.
kc [GPL] -- transforms chemical equations into simulation programs.
Kemistry [GPL] -- a collection of chemistry-related applications for KDE.
KMol [GPL] -- a molecular weight and elemental composition calculator.
KMovisto [GPL] -- a molecule viewer which reads GAUSSIAN files and exports POV-Ray scripts.
LASSAP -- an extensible, high performance , parallel sequence comparison software.
Lennard-Jones Gas Simulation [GPL] -- using molecular dynamics.
LigBuilder -- a multiple-purposed program written for structure-based drug design procedure.
NEW Linux for Biotechnology [GPL] -- Biotechnology related software pre-compiled for Linux.
NEW MacroModel [CM] -- construction of chemical structures and application of molecular mechanics/dynamics.
Maestro [CM] -- state-of-the-art graphical interface for molecular modeling.
Mage -- a browser called for kinemage file format.
NEW Marvin [CM] -- a set of Java tools for drawing and displaying chemical structures.
MEXICO -- a program for calculating lineshapes in the NMR spectrum of exchanging species.
Microsat -- a microsatellite distance calculation program.
MidasPlus [CM] -- an advanced molecular display and simulation system.
MIPSIM -- molecular interaction potentials and molecular similarity calculations.
Molecular Modeling Toolkit -- a library for molecular modeling.
MODELLER -- a program for homology protein structure modelling by satisfaction of spatial restraints.
MOE [CM] -- a flexible and powerful software environment for chemical computing.
MOISS [GPL] -- a n-particle, n-dimensions Monte Carlo Schroedinger equation integrator.
Molaris -- macromolecular simulation to study the functions of proteins.
Molden -- a pre- and post processing program of molecular and electronic structure.
MOLCAS [CM] -- a quantum chemistry software for molecular systems.
Moldy [GPL] -- 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.
MOSCITO [GPL] -- molecular dynamics simulation of condensed phase systems.
MPQC [GPL] -- massively parallel quantum chemistry program.
MSMS -- compute efficiently triangulations of Solvent Excluded Surfaces.
NAMD -- parallel, object-oriented molecular dynamics program.
NanoCAD [GPL] -- 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.
nuees -- perform ATD and classification.
NWChem -- high performance computational chemistry software.
OPIUM -- analysis of solution equilibria, determination of chemical model, etc.
ORAC [GPL] -- a molecular dynamics program to simulate solvated biomolecules.
ORTEP-III -- drawing crystal structure illustrations.
OSET [GPL] -- a Computer-Assisted Organic Synthesis program for retrosynthetic analysis.
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.
PCMODEL [CM] -- a complete molecular modeling package for research chemists.
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.
Populations [GPL] -- a population genetic software.
PovChem -- generates POV-Ray files from Protein Data Bank.
PQS [CM] -- high performance parallel quantum chemistry software for Linux (single or cluster).
NEW Protein Explorer -- view and explore the 3D structure of any macromolecule.
Protein Structure Software -- programs and C libraries.
PROCHECK -- programs to check the stereochemical quality of protein structures.
PUZZLE -- reconstructs phylogenetic trees from molecular sequence data by maximum likelihood.
PyMOL -- a molecular graphics system with an embedded Python interpreter.
Q-Chem [CM] -- an ab initio quantum chemistry software product.
Q2 -- a chemometric toolbox.
QCPE LINUX Software Program [CM] -- several quantum chemistry programs.
QikProp [CM] -- rapid predictions for physical and pharmaceutical properties of neutral organic molecules.
Qmol -- molecular Viewer for structure and trajectory data.
RasMol -- molecular graphics program intended for the visualisation.
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 [GPL] -- produces position specific reliability prediction for any protein sequence alignment.
SCORE -- evaluate the binding affinity of protein-ligand complex with known 3D structure.
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.
NEW SimBioSys Products [CM] -- rational drug design software for design/optimization of small, organic therapeutics.
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.
Swiss_PDBViewer -- a user friendly interface to analyse several proteins at the same time.
tacg -- command line tool for the restriction enzyme analysis of DNA.
TheRate -- an intuitive teaching tool for courses in applied quantum chemistry and kinetics.
Thermo-Calc [CM] -- a software package for thermodynamics equilibrium and phase diagram calculations.
TINKER -- a package for molecular mechanics and dynamics of molecules, especially polypeptides.
NEW treeplot [GPL] -- converting phylogenetic tree file to vector or image file.
Turbo Frodo and Turbo X [CM] -- 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.

VASP Data Viewer [GPL] -- a 3D viewer for molecular charge distributions from VASP.
VEGA -- to bridge between most molecular software and to manipulate 3D structures.
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 [CM] -- a versatile protein structure analysis program.
WIEN97 [CM] -- perform electronic structure calculations of solids using LAPW method.
WinMGM -- a molecular graphism program.
Wise2 [GPL] -- 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.
XCrySDen -- a molecular and crystalline structure rendering program.
XEASY [CM] -- NMR spectrum analysis.
xelem -- displays a hypertext periodic table with many information.
XEMR -- a software package written for electron magnetic resonance (EMR) spectroscopists.
NEW XMakemol [GPL] -- a program for viewing and manipulating atomic/molecular systems.
XMolCalc -- a small utility that allows you to calculate a molecular weight.
XNBC -- simulating biological neural networks.
XNMR [SR] -- a program for processing NMR spectra.
XLOGP/PLOGP -- calculation of logP of common organic compounds and peptides.
X-PLOR [CM] -- computational structural biology, X-ray crystallography and NMR.
XtalView -- solving a macromolecular crystal structure by isomorphous replacement.
xyz2rgb [GPL] -- a tool for animating molecules.

Also Check Out:
AFNI -- software for analysis of functional neuroimages.
ANALYZE [CM] -- multimodality, multidimensional biomedical imaging and visualization.
BALSAC [CM] -- build and analyze lattices, surfaces, and clusters.
DRAWxtl -- display crystal structures in VRML or POV-RAY raytracer.
DPMTA -- distributed parallel multipole tree algorithms.
Electronic Periodic Table of the Elements
Montage -- a serial-reconstruction package that reconstructs serial data in 3 dimensions.
NeuronC -- a neural simulator language.
PenguMetrics [GPL] -- software collection for the operation of optical (UV/VIS/NIR) spectrometers.
Pixies -- an application for biomedical image analysis with sophisticated tools.
SHELX -- a set of programs for crystal structure determination from single-crystal diffraction data.
xcosm -- removing out-of-focus light in 3-D volumes collected plane by plane.

Other Resources: -- helps you to find chemistry and chemical engineering related terms, definitions, synonyms, acronyms and abbreviations. Also search forms for finding MSDS/safety data, scientific publications in over 20.000 different journals, physical data of chemical compounds, worldwide patents and spectral data are available.


Linux and Chemistry : Links to chemistry software on Linux.

Web Sites in Inorganic Chemical Thermodynamics

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

Links for Chemists: The Chemistry section of The WWW Virtual Library

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