Life & Material Sciences applications

• ApoCom Grail Toolkit for Genomics (ACTG) [LS]  - (tool for DNA sequence analysis and database searches from a common graphical user interface)
  ApoCom Genomics
• bioSCOUT [LS] - (automated gene and genome analysis) LION Bioscience AG
• DecisionSite for Functional Genomics [LS] - (Display and analysis tool for early stage research and bioinformatics activities)
  Spotfire, Inc.
• Derwint GENESEQ  [LS] - (Database of patented nucleic acid and protein sequences; developed as a cooperative effort between GCG and Derwint Publications Ltd.) Thomson Derwent
• Finch Sequencing Center [LS] - (Components for integrating public domain analysis tools)
  Geospiza, Inc.
• GCG Wisconsin Package [LS] - (More than 120 interrelated software programs for database searching, sequence comparison, pattern searching, primer selection, sequence assembly, protein analysis, evolutionary analysis, and secondary protein structure) Accelrys, Inc. [LS] - (includes wholly owned subsidiary Genetics Computer Group)
• GenoMax  [LS] - (Enterprise software for the high-throughput research environment, designed with the ResearchLogic knowledge base)
  InforMax, Inc.
• JDA Intellect [LS] (Suite of data mining technologies)
  JDA Software Group
• LifeSeq Gold [LS] - (Tool for drug discovery and development)
  Incyte Genomics
• LSF [LS] - (Integrated suite of workload management products)
  Platform Computing Corporation
• Oracle7, Oracle8i, Oracle9i, Oracle 10g, Oracle 11i [LS] - (Relational database management systems and tools)
  Oracle Corporation
• SeqLab [LS] - (X Windows interface to the GCG Wisconsin Package)
  Accelrys, Inc. - (Includes wholly owned subsidiary Genetics Computer Group)
• SeqWeb [LS] - (Provides access to the GCG Wisconsin Package through Netscape or Internet Explorer web browser on local intranet)
  Accelrys, Inc. - (Includes wholly owned subsidiary Genetics Computer Group)
• SPS Cross_Match [LS] - (Parallel version of Cross_Match) Southwest Parallel Software, Inc.
• SPS Phrap [LS] (Parallel version of Phrap)
  Southwest Parallel Software, Inc.
• SPS SWAT [LS] (Parallel version of SWAT)
  Southwest Parallel Software, Inc.
• SRS Evolution [LS] - (Bioinformatics querying package) LION Bioscience AG
• Vector NTI Advance [LS] - (Desktop sequence analysis system)
  InforMax, Inc.
• ZooSeq  [LS] - (Tool for drug discovery and development) Incyte Genomics

• ACCORD [L+MS] - (chemical data management) Accelrys, Inc.
• Cambridge Structural Database [L+MS] - (Small-molecule crystal structures database) Cambridge Crystallographic Data Centre
• DIVA[L+MS] -(Visualization and analysis of chemical and biological data) Accelrys, Inc.
• DSSP [LS] -(Database of secondary structure in proteins) European Molecular Biology Laboratory (EMBL)
• Protein Data Bank (PDB) [LS] - (Archive of biological macromolecule structures) Rutgers University
• QUEST3D [MS] (Search engine for the CSD) Cambridge Crystallographic Data Centre (CCDC)
• RS3 Discovery[L+MS] - (Server for chemical structure storage, searching, and retrieval) Accelrys, Inc.
• RS3 Discovery HTS [L+MS] (Data storage and analysis for high throughput screening) Accelrys, Inc.
• SQL*LIMS [MS] -(Cheminformatics) Applied Biosystems
• UNITY [LS] - (Cheminformatics) Tripos, Inc.

• eClinical Platform - (Collection and distribution of clinical trial data) etrials
• Oracle Clinical [LS] -(Pharmaceutical clinical trials solution) Oracle
• S-PLUS® [LS] -(Solution for exploratory data analysis and statistical data mining) Insightful Corporation
• S+SeqTrial [LS] -(An S-PLUS software library for designing, monitoring, and analyzing clinical trials using group sequential methods)

• ACES II [MS] - (Ab initio electronic structure calculation) University of Florida Quantum Theory Project
• AMBER [LS] -(Molecular simulation package) UCSF, The Scripps Research Institute
• AMPAC 6.0 [MS] -(General purpose semi-empirical quantum mechanical package) Semichem, Inc.
• AMSOL [MS] -(Semiempirical quantum chemistry program) MakoLab
• AutoDock [LS] -(Automated docking of flexible ligands to macromolecules) The Scripps Research Institute
• Bielefeld Protein Docking [LS] -(Docking) University of Bielefeld
• BOSS [LS] - (Simulation of solute molecules in solvent and standard molecular mechanics modeling) Yale University Department of Chemistry
• CADPAC [L+MS] - (ab initio quantum chemistry code) Cambridge University Centre for Computational Chemistry, CUC3
• CASTEP [L+MS] -(Ab initio code for the solution of the electronic ground state of periodic systems) Accelrys, Inc.
• CAVEAT [MS] -(De novo design of organic molecules) University of California, Berkeley
• CCP4 [LS] -(Crystallography software) Daresbury Laboratory
• CHARMm [LS] - (Molecular modeling package) Accelrys, Inc.
• Chimera [LS] - (GUI molecular modeling package) Thomas E. Ferrin, University of California, San Francisco (UCSF) Computer Graphics Laboratory
• CODESSA [MS] -(Quantitative structure/activity relationship program) Semichem
• CoMFA [MS] -(Quantitative structure/activity relationship program) Tripos, Inc.
• CPMD [MS] -(Quantum mechanics) CPMD Consortium
• Crystal03 [MS] -(Electronic structure of periodic systems) the Computational Materials Science Group, Daresbury Laboratory and the Theoretical Chemistry Group at the University of Torino
• DIVA [LS] -(Visualization and analysis of chemical and biological data) Accelrys, Inc.
• DGeom [LS] -(Distance geometry chemistry code) Quantum Chemistry Program Exchange (QCPE)
• Discover [L+MS] -(Molecular simulation) Accelrys, Inc.
• DL_POLY [L+MS] -(Parallel molecular dynamics simulation package) Daresbury Laboratory
• DMol3 [L+MS] -(Quantum mechanical program) Accelrys, Inc.
• DOCK [LS] -(Docking) UCSF
• DOT [LS] -(Docking) UCSD
• ENZYMIX [LS] -(Macromolecular simulation program) Professor Arieh Warshel
• GAMESS US [L+MS] - (ab initio quantum chemistry package) Iowa State University (ISU) Ames Laboratory
• GAMESS-UK [L+MS] -(enhanced version of GAMESS) Computing for Science Ltd, CCLRC Daresbury Laboratory
• Gaussian 03 [L+MS] -(electronic structure program) Gaussian Inc.
• GRAMM [LS] -(docking) SUNY at Stony Brook
• GROMACS [LS] -(molecular dynamics) Groningen University
• GROMOS [LS] -(molecular dynamics simulation) Laboratory of Physical Chemistry, ETH
• ICM [LS] -(shell providing range of molecular modeling, statistics, and other functions) Molsoft LLC, Inc.
• Jaguar (formerly PS-GVB) [L+MS] - (ab initio quantum chemistry code) Schrödinger, Inc.
• LEaP [LS] -(model builder for use with AMBER) James W. Caldwell, University of California San Francisco
• MacroModel [L+MS] Schrödinger, Inc.
• Materials Studio [MS] -(materials simulation) Accelrys, Inc.
• MCPRO [LS] -(monte carlo simulations for proteins and peptides) Department of Chemistry, Yale University
• MICE [LS] Dr. Charles Carter, University of North Carolina
• MidasPlus [LS] -(molecular modeling package) Thomas E. Ferrin, University of California San Francisco Computer Graphics Laboratory
• MM3 [LS] -(molecular modeling code) Computational Center for Molecular Structure and Design (CCMSD), University of Georgia
• MOE [LS] -(Molecular Operating Environment) (suite of modeling applications complete with Scientific Vector Language) Chemical Computing Group, Inc.
• MOLCAS [L+MS] (ab initio quantum chemistry code) Department of Theoretical Chemistry, University of Lund, Sweden
• MOLPRO [L+MS] - (quantum chemistry package) University of Cardiff
• MOPAC 2002 [L+MS] -(semi-empirical electronic modeling of molecular systems) developed by Dr James J P Stewart Available from: Schrödinger, Inc., CaChe Group (Fujitsu America), and Fujitsu (elsewhere)
• MOZYME [MS] -(semi-empirical electronic modeling of molecular systems) Fujitsu
• NONMEM [MS] -(quantitative structure/activity relationship program) GloboMax Service Group
• NWChem [MS] -(quantum mechanics, molecular mechanics) PNNL
• OpenEye [LS] OpenEye Scientific Software
• PCMODEL [MS] -(molecular modeling) Serena Software
• Polaris [LS] - (free energies and electrostatic properties of solutes) Professor Arieh Warshel
• Q-Chem [L+MS] -(quantum chemistry software) Q-Chem, Inc.
• QuaSAR [MS] - (quantitative structure/activity relationship program) Chemical Computing Group
• ROCS [LS] - (docking) OpenEye Scientific Software
• Spartan [L+MS] -(GUI computational chemistry package) Wavefunction Inc.
• SYBYL [MS] -(Semiempirical, Molecular Mechanics) Tripos, Inc.
• TINKER [LS] -(molecular mechanics/dynamics code) Washington University
• TURBOMOLE [L+MS] -(Package for ab initio electronic structure calculations) Quantum Chemistry Group, University of Karlsruhe, Germany
• VAMP [L+MS] -(semi-empirical package for quantum-mechanical calculations) University of Erlangen & Technische Universität Wien, distributed by Accelrys, Inc.
• VASP [L+MS] - (ab initio package for quantum-mechanical calculations) Institute for Theoretical Physics, Vienna University of Technology, Austria
• VIDA [LS] (Docking)

Genetic sequencing identifies the exact DNA sequence in a region of a chromosome or a whole chromosome. Applications on HP's platforms include:

• Ace.mbly [LS] - (graphic interactive program to support shotgun and directed sequencing projects)
  Centre de Recherches de Biochimie Macromoleculaire du CNRS, Montpellier University, France
• Bass [LS] - (lane tracking and base calling on UNIX)
  Whitehead Institute (MIT Center for Genome Research)
• BioXL [LS] - (hardware search accelerator for GenCore range) Compugen Ltd.
• BLAST: see WU-BLAST and NCBI-BLAST
• ClustalW [LS] - (sequence analysis)
  European Molecular Biology Network
• Coils [LS] - (protein sequence analysis)
  European Bioinformatics Institute
• Compugen ParSeq [LS] - (software-only accelerator for GenCore range)
  Compugen Ltd.
• Consed [LS] - (sequence assembly editor for use with PHRAP)
  University of Washington Genome Center
• Cross_Match [LS] - (general-purpose utility for comparing two sets of DNA sequences)
  Geospiza, Inc.
• EMBOSS [LS] - (biology toolkits for sequence analysis)
  EMBnet
• EXP6 [LS] - (gene sequence analysis)
  Genomix Corp.
• FastA [LS] - (sequence similarity database search tool)
  University of Virginia
• FingerPrintScan [LS] - (protein sequence analysis)
  University of Manchester
• GenCore [LS] - (high throughput sequence analysis package)
  Compugen Ltd.
• GeneMark [LS] - (gene sequence analysis)
  Georgia Tech
• GeneMine [LS] - (gene sequence analysis)
  UCLA
• GenePort [LS] - (portal-based interface to view Genomic data)
  Incogen
• GeneScan [LS] - (gene sequence analysis)
  Stanford University
• GeneQuiz [LS] - (large scale sequence analysis)
  EMBL - European Bioinformatics Institute
• GRAIL [LS] - (AI system for gene recognition and interpretation)
  Oak Ridge National Laboratory Computational Biology section)
• GRM (Genome Reconstruction Manager) [LS] -
  (semi-automatic reconstruction of DNA sequences from sequence data and directed or constraint data)
  (Baylor College of Medicine Human Genome Sequencing Center)
• HMMER [LS] - (Hidden Markov model)
  Washington U. Department of Genetics
• InterProScan [LS] - (protein sequence analysis)
  European Bioinformatics Institute
• LifeSeq Gold [LS] - (database of gene sequence and expression information for 1.3 million human gene fragments)
  Incyte Genomics, Inc.
• MASE [LS] - (Multiple Alignment Sequence Editor)
  BioMolecular Engineering Research Center, Boston University
• MatchMaker [LS] - (gene sequence analysis)
  Tripos, Inc.
• MEME [LS] - (gene sequence analysis)
  UCSD
• MSEARCH [LS] - (parallel sequence databases searching)
  Pittsburgh Supercomputing Center Biomedical Initiative
• NCBI-BLAST [LS] - (fast sequence similarity database search tools)
  NCBI
• Paup 4.0 [LS] - (phylogenetic analysis - molecular evolution)
  Florida State University
• pfscan [LS] - (protein sequence analysis)
  ISREC (Swiss Institute for Experimental Cancer Research)
• Phrap [LS] - (fragment assembly program)
  Geospiza, Inc.
• Phred [LS] - (base-calling software with quality information)
  Geospiza, Inc.
• PHYLIP [LS] - (phylogenetic analysis - molecular evolution)
  University of Washington
• PIMA.SH [LS] - (Pattern-Induced Multiple-sequence Alignment program)
  BioMolecular Engineering Research Center, Boston University
• ppsearch [LS] - (protein sequence analysis)
  European Bioinformatics Institute
• RepeatMasker [LS] - (gene sequence analysis)
  Geospiza, Inc.
• Sim4 [LS] - (gene sequence analysis)
  Pennsylvania State University
• Staden Package [LS] - (sequence assembly and editing program)
  Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge
• SWAT [LS] - (sequence alignment tool)
  Geospiza, Inc.
• T-Coffee [LS] - (global or local sequence alignment)
  CNRS
• TurboBLAST [LS] - (an accelerated parallel deployment of NCBI BLAST)
  TurboGenomics
• Wisconsin Package [LS] - (comprehensive genetic sequencing tools)
  Accelrys, Inc.
• Wise2 [LS] - (gene sequence analysis)
  Wellcome Trust Sanger Institute
• WU-BLAST [LS] - (fast sequence similarity database search tools)
  Washington University

• AVIS (MS) - visualization of complex data
• Chimera [LS] - (GUI molecular modeling package)
  Thomas E. Ferrin, University of California San Francisco Computer Graphics Laboratory
• ICM [LS] - (shell providing range of molecular modeling, statistics, and other functions)
  Molsoft LLC, Inc.
• GaussView [L+MS] - (graphical user interface for Gaussian)
  Gaussian Inc.
• GRASP [LS] - (molecular visualisation and analysis)
  Columbia University
• LEaP [LS] - (model builder for use with AMBER)
  James W. Caldwell, University of California San Francisco
• Maestro [L+MS] - (graphical user interface for Schrodinger products)
  Schrödinger, Inc.
• MOE (Molecular Operating Environment) [LS] - (suite of modeling applications complete with Scientific Vector Language)
  Chemical Computing Group, Inc.
• RasMol [LS] - (3D molecular structure viewer)
  University of Edinburgh and University of Massachusetts
• Raster3D [LS] - (photorealistic molecular modeling)
  Ethan A. Merritt, University of Washington
• Ribbons [LS] - (interactive display and creation of publication-quality molecular modeling images)
  Mike Carson, UAB Center for Biophysical Sciences and Engineering (previously known as the UAB Center for Macromolecular Crystallography)

Physical mapping creates, places, and locates markers on chromosomes to act as "landmarks". Linkage analysis identifies markers and locations along the chromosome that, through pedigree studies in large families, can be linked to target (typically disease) genes. Applications on HP's platforms include: 

• AceDB [LS]
  (genomic database system)
  Sanger Institute
• CRI-MAP [LS]
  (construction of multi-locus linkage maps)
  Dr Phil Green, University of Washington
• CRI-MAP-PVM [LS]
  (parallelized version of CRI-MAP)
  Tara Matise 
• FASTLINK [LS]
  (linkage analysis - faster version of LINKAGE)
  Oxford University
• Gene Hunter [LS]
  (complete multi-point linkage analysis, including halotyping)
  Whitehead Institute (MIT Center for Genome Research)
• LINKAGE [LS]
  (package for calculation of recombination rates, lod score tables and genetic risks)
  Mark Lathrop, J. Lalouel, C. Julier, Jurg Ott, Alan Young, Daniel Weeks
• MAPMAKER [LS]
  (constructs genetic maps)
  Whitehead Institute (MIT Center for Genome Research)
• Primer3 [LS]
  (picks primers for PCR reactions)
  Whitehead Institute (MIT Center for Genome Research)
• QUICKMAP [LS]
  (database and navigation tool for integration of CEPH-Généthon data)
  Centre d'Etude du Polymorphisme Humain (CEPH)
• RHMapper [LS]
  (optimization tool for radiation hybrid maps)
  Whitehead Institute (MIT Center for Genome Research)
• S-PLUS [LS]
  (solution for exploratory data analysis and statistical data mining)
  Insightful Corporation
• S+SeqTrial [LS]
  (S-PLUS software library for designing, monitoring, and analyzing clinical trials using group sequential methods)
  Insightful Corporation
• Sigma [LS]
  (genetic mapping workbench)
  Center for Human Genome Studies at LANL
• STS-Pipeline [LS]
  (removes vector sequences and identifies duplicates)
  Whitehead Institute (MIT Center for Genome Research)
• Vitesse [LS]
  (calculates likelihood on pedigrees)
  Contact:  Jeff O'conell 
  

• CITI2/BISANCE [LS]
  (genetics and imaging software library)
  CITI2, Université René Descartes, France
• EMBL Suite [LS]
  (suite of genetic sequencing applications)
  European Molecular Biology Laboratory (EMBL)
• MBCRR Package [LS]
  (DNA and protein sequencing and structural analysis)
  The Molecular Biology Computer Research Resource (MBCRR) at the Dana-Farber Cancer Institute and the School of Public Health, Harvard University.

• ARP/wARP [LS]
  (automated refinement mapping)
  EMBL
• Buster (recovers missing phase information in X-ray crystallography)
  Global Phasing Ltd.
• CCP4 [LS]
  (crystallography software)
  The Daresbury Laboratory
• CNS [LS]
  (Crystallography & NMR System)
  Yale University
• DENZO [LS]
  (processes raw X-ray diffraction data)
  Zbyszek Otwinowski, Southwestern Medical Center, University of Texas, Wladek Minor, University of Virginia
• DPS [LS]
  (data processing suite for crystallographic area detector data)
  Purdue University
• EXPO [MS]
  (extraction of integrated intensities from a powder diffraction pattern and crystal structure solution via Direct Methods)
  Istituto di Ricerca per lo Sviluppo di Metodologie Cristallografiche (CNR)
• GSAS [L+MS]
  (crystallography)
  LANL
• HKL [L+MS]
  (crystallography)
  HKL Research, Inc.
• MAIN [LS]
  (Crystallography & NMR System)
  Josef Stefan Institute
• MLPHARE [LS]
  (maximum likelihood heavy atom refinement and phase calculation)
  Zbyszek Otwinowski, Southwestern Medical Center, University of Texas
• MolScript [LS]
  (creates 3D pictures of molecules in wide range of formats)
  Avatar Software AB
• MOSFLM [LS]
  (crystallography)
  MRC Laboratory of Molecular Biology
• O [LS]
  (Crystallographic refinement and filtering)
  Uppsala University, Sweden
• Protein Data Bank (PDB) [LS]
  (archive of biological macromolecule structures)
  Rutgers University
• RasMol [LS]
  (3D molecular structure viewer)
  University of Edinburgh and University of Massachusetts
• Raster3D [LS]
  (photorealistic molecular modeling)
  Ethan A. Merritt, University of Washington
• RAVE [LS]
  (crystallography package)
  Uppsala University
• RESOLVE [LS]
  (crystallography)
  Los Alamos National Laboratory
• Ribbons [LS]
  (interactive display and creation of publication-quality molecular modeling images)
  Mike Carson, UAB Center for Biophysical Sciences and Engineering (previously known as the UAB Center for Macromolecular Crystallography)
• RSRef [L+MS]
  (package for the refinement of an atomic model into electron density)
  Dr. Michael S. Chapman, Florida State University
• SHARP [LS]
  (statistical heavy atom refinement and phasing for crystallography)
  Global Phasing Ltd.
• SHELX [L+MS]
  (programs for crystal structure determination from single-crystal diffraction data)
  University of Göttingen
• SHELXL [LS]
  (twin refinement)
  University of Göttingen
• SIR97 [MS]
  (resolution and refinement of crystal structures using single crystal data)
  Istituto di Ricerca per lo Sviluppo di Metodologie Cristallografiche (CNR)
• SOLVE [LS]
  Tom Terwillinger, Los Alamos National Laboratory
• SnB [LS]
  ('Shake and Bake' crystal structure determination application)
  Hauptman-Woodward Medical Research Institute, Inc.
• SQUASH [LS]
  (crystallographic tool for phase refinement and extension on large structures)
  Professor David S. Eisenberg, Molecular Biology Institute, UCLA
• TNT [LS]
  (automated optimization of X-Ray crystallography models)
  Lynn F. Ten Eyck, San Diego Supercomputer Center and Brian W. Matthews, University of Oregon
• Triad [LS]
  (NMR)
  Tripos, Inc.
• TurboFrodo [LS]
  (General-purpose molecular modeling environment)
  Centre National de la Recherche Scientifique (CNRS)
• wARP [LS]
  (automated refinement mapping)
  EMBL
• X-PLOR [LS]
  (macromolecular modeling from X-ray diffraction and NMR data)
  Academic users contact: Yale University
  Commercial users contact: Accelrys, Inc.
• XDS [MS]
  (crystallography)
  Max-Planck Institute
• XtalView [LS]
  (crystallography package for fitting electron density maps and solving structures)

Finally, a few applications that don't fit neatly into any of these categories:

• BioPerl [LS]
  (biology toolkit)
  The BioPerl Project
• BMERC Library [LS]
  (Biomolecular Engineering Research Center Library)
  Boston University
• CHEMKIN [MS]
  (chemical factory modeling)
  Reaction Design
• Physiolab [LS]
  (biosimulation technology for in silico R&D)
  Entelos, Inc.
• SPIDER [LS]
  (electron microscope imaging)