TOPIC AREAS

MICROBIOLOGY

RESOURCES

showcases relevant applications.

ABaCUS -- investigate the significance of the putative correspondence between exons and units of protein structure.
Acedb -- a genome database system.
ADF  -- Amsterdam Density Functional program for computational chemistry research.
AMBER  -- simulation of biomolecules and molecular simulation programs.
AMMP  -- 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.
BioJava  -- providing Java tools for processing biological data.
BioMail  -- 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  -- a bioinformatics template C++ library.
CACTVS Tools -- A visualization package for chemist.
Catacomb  -- frameworks for various types of models in neuroscience.
CDA -- analyze chemical systems which can be described as donor-acceptor complexes.
ChemApp -- a programmable thermodynamic calculation interface.
ChemCalc  -- a calculator that is more oriented towards chemistry.
chemeq  -- translate chemical equations to LaTeX code.
ChemSol -- calculates solvation free energies with Langevin Dipoles solvation model.
Chemsuite  -- molecular 2/3D drawing and chemical reaction simulation software.
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.
CHIMP  -- a generic tool for the modeling of chemical phenomena.
Clarrhmos  -- 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.
Chemical Resource Kit -- 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.
DNA/GUI -- GUI for quantitative imaging and analysis of electrophoretic gels and autoradiograms.
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.
E-Cell -- a modeling and simulation environment for biochemical and genetic processes.
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.
Garlic  -- a free/open source molecular visualization program for UNIX/Linux.
Gaussian  -- an electronic structure program for chemists.
gBioSeq -- a graphical multiple DNA sequence alignment editor.
GDE -- a set of programs for multiple sequence alignment and analysis.
gdis  -- a GTK based program for visualizing molecules and periodic systems.
gdpc  -- a program for visualising molecular dynamic simulations.
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.
Genpak  -- a set of small utilities to manipulate DNA sequences in a Unix fashion.
GENSPECT -- spectral toolbox for calculating spectral properties of gases.
GERM  -- genetically evolved receptor models.
Ghemical  -- 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.
GP/Arka  -- a set of small utilities to manipulate DNA sequences and a GUI program.
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.
GtkChemkin  -- handles save-files written by the chemkin program.
GULP -- simulation on 3D periodic solids, gas phase clusters and isolated defects in a bulk material.
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.
JChem -- a development tool in Java for manipulating mixed chemical and corporate data.
JChemPaint  -- a program for drawing 2D chemical structures, written in Java.
JCFL  -- Java library for utilizing Chemical Markup Language (CML).
Jmol  -- an open-source molecule viewer and editor.
kc  -- transforms chemical equations into simulation programs.
Kemistry  -- a collection of chemistry-related applications for KDE.
KMol  -- a molecular weight and elemental composition calculator.
KMovisto  -- 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  -- using molecular dynamics.
LigBuilder -- a multiple-purposed program written for structure-based drug design procedure.
Linux for Biotechnology  -- Biotechnology related software pre-compiled for Linux.
MacroModel  -- construction of chemical structures and application of molecular mechanics/dynamics.
Maestro  -- state-of-the-art graphical interface for molecular modeling.
Mage -- a browser called for kinemage file format.
Marvin  -- 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  -- 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  -- a flexible and powerful software environment for chemical computing.
MOISS  -- 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  -- 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.
MOSCITO  -- molecular dynamics simulation of condensed phase systems.
MPQC  -- massively parallel quantum chemistry program.
MSMS -- compute efficiently triangulations of Solvent Excluded Surfaces.
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.
nuees -- perform ATD and classification.
NWChem -- high performance computational chemistry software.
OPIUM -- analysis of solution equilibria, determination of chemical model, etc.
ORAC  -- a molecular dynamics program to simulate solvated biomolecules.
ORTEP-III -- drawing crystal structure illustrations.
OSET  -- 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  -- 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  -- a population genetic software.
PovChem -- generates POV-Ray files from Protein Data Bank.
PQS  -- high performance parallel quantum chemistry software for Linux (single or cluster).
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  -- an ab initio quantum chemistry software product.
Q2 -- a chemometric toolbox.
QCPE LINUX Software Program  -- several quantum chemistry programs.
QikProp  -- 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  -- 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.
SimBioSys Products  -- 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  -- a software package for thermodynamics equilibrium and phase diagram calculations.
TINKER -- a package for molecular mechanics and dynamics of molecules, especially polypeptides.
treeplot  -- converting phylogenetic tree file to vector or image file.
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. VASP Data Viewer  -- 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  -- a versatile protein structure analysis program.
WIEN97  -- perform electronic structure calculations of solids using LAPW method.
WinMGM -- a molecular graphism program.
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.
XCrySDen -- a molecular and crystalline structure rendering program.
XDrawChem -- a two-dimensional molecule drawing program for Unix operating systems.
XEASY  -- NMR spectrum analysis.
xelem -- displays a hypertext periodic table with many information.
XEMR -- a software package written for electron magnetic resonance (EMR) spectroscopists.
XMakemol  -- 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  -- a program for processing NMR spectra.
XLOGP/PLOGP -- calculation of logP of common organic compounds and peptides.
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.

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