| Database | WWW-Address | Descriptions |
| EMBL | http://www.ebi.ac.uk/embl/ | European Molecular Biology Laboratory nucleotide sequence database at EBI, Hinxton, UK |
| GenBank | http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html | DNA Genome Sequence Database at National Center for Biotechnology information, NCBI, Bethesda, MD, USA |
| DDBJ | http://www.ddbj.nig.ac.jp/ | DNA Data Bank Japan at CIB , Mishima, Japan |
| SWISS-PROT/TrEMBL | http://www.expasy.ch/ | Protein Sequence Database (Swiss Institute of Bioinformatics, SIB, Geneva, CH |
| PIR-PSD | http://pir.georgetown.edu/pirwww/search/textpsd.shtml | PIR-International Protein Sequence Database, annotated protein database by PIR, MIPS and JIPID at NBRF, Georgetown University, USA |
| SRS | http://srs.ebi.ac.uk/ | Sequence Retrieval System |
| Database | WWW-Address | Descriptions |
| DbEST | http://www.ncbi.nlm.nih.gov/dbEST/index.html | Database of Expressed Sequence Tags at NCBI, USA |
| TIGR | http://www.tigr.org/tdb/tgi.shtml | TIGR Genome Indices, integrated analysis of public EST data, TIGR, USA |
| DbSNP | http://www.ncbi.nlm.nih.gov/SNP/ | Database of Single Nucleotide Polymorphism at NCBI, USA |
| CluSTr | http://www.ebi.ac.uk/clustr/ | Clusters of SWISS-PROT and TrEMBL proteins at EBI, UK |
| ProtoMap | http://www.protomap.cs.huji.ac.il/ | Hierarchical classification of all Swiss-Prot proteins |
| PROSITE | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_prosite.html | Prosite Protein functional pattern database |
| PRODOM | http://prodes.toulouse.inra.fr/prodom/doc/prodom.html | The Protein Domain Database |
| PFAM | http://www.sanger.ac.uk/Pfam/ | Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families |
| Database | WWW-Address | Descriptions |
| PDB | http://www.rcsb.org/pdb/index.html | Protein structural Data Bank cured by Research Collaboratory of Structural Bioinformatics By Rutgers, SDSC and NIST, USA |
| NDB | http://ndbserver.rutgers.edu/NDB/ndb.html | Nucleic Acid structure Datatabase at Rutgers University , USA |
| EBI-MSD | http://msd.ebi.ac.uk/ | Macromolecular Structure Database at EBI, UK |
| CSD | http://cds3.dl.ac.uk/cds/crystal.html | The Cambridge Structural Database of small-molecule crystal structures |
| Database | WWW-Address | Descriptions |
| SCOP | http://scop.mrc-lmb.cam.ac.uk/scop/ | Structural Classification of Proteins |
| CATH | http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html | Protein Structure Classification (Class Architecture Topology and Homologous superfamily) |
| 3Dee | http://circinus.ebi.ac.uk:8080/3Dee/help/help_intro.html | A Database of Protein Domain Definitions |
| FSSP | http://www2.ebi.ac.uk/dali/fssp/ | Fold Classification based on Structure-Structure alignment of Proteins |
| TOPS | http://bioinformatics.leeds.ac.uk/~tops/ | Protein structural topology and protein topology Cartoons |
| HOMSTRAD | http://www-cryst.bioc.cam.ac.uk/~homstrad/ | Homologous Structure Alignment Database |
| PASS2 | http://www.ncbs.res.in/%7Efaculty/mini/campass/pass.html | Semi-Automated database of Protein Alignments organised as Structural Superfamilies |
| DIP | http://dip.doe-mbi.ucla.edu/ | Database of Interacting Proteins |
| Program | WWW Address | Program Name |
| Fasta3 | http://www.ebi.ac.uk/fasta3/ | Sequence similarity and homology searching against nucleotide and protein database using Fasta3 (Global Alignment) |
| BLAST2 | http://www.ebi.ac.uk/blastall/ | NCBI blast2 (blastall) program (Local Alignment) |
| Blitz (bic_sw) | http://www.ebi.ac.uk/bic_sw/ | Compugen Bic2 Smith & Waterman algorithm Implementation for protein database searches (Local Alignment) |
| MPsrch | http://www.ebi.ac.uk/MPsrch/ | Edinburgh University new implementation of the Smith and Waterman algorithm (Local Alignment) |
| Scanps2.3 | http://www.ebi.ac.uk/scanps/ | Fast implementation of the true Smith & Waterman algorithm for protein database searches (Local Alignment) |
| PSI/PHI-BLAST | http://www.ncbi.nlm.nih.gov/BLAST/ | (Position Specific/Pattern Hit)Iterated BLAST (Local Alignment) |
| Dotlet | http://www.isrec.isb-sib.ch/java/dotlet/Dotlet.html | A Java applet for sequence comparisons using the dot matrix method |
| REP | http://www.embl-heidelberg.de/~andrade/papers/rep/search.html | Searches a protein sequence for a repeats |
| Program | WWW-Address | Program Description |
| SMART | http://smart.embl-heidelberg.de/ | Domain Assignment (Oxford/EMBL) |
| PFAM | http://www.sanger.ac.uk/Software/Pfam/ | (Sanger Centre/Wash-U/Karolinska Institute) |
| COGs | http://www.ncbi.nlm.nih.gov/COG/ | Phylogenetic classification of proteins encoded in complete genomes |
| PRINTS | http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ | PRINTS is a compendium of protein fingerprints |
| PRODOM | http://prodes.toulouse.inra.fr/prodom/doc/form.html | Protein Domain families. |
| BLOCKS | http://blocks.fhcrc.org/blocks/blocks_search.html | Multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins |
| InterPro | http://www.ebi.ac.uk/interpro/ | Integrated documentation resource for protein families, domains and functional sites. |
| SWISPROT | http://us.expasy.org/sprot/ | Domain description in the annotations. |
| CD-Search | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi | Search for Conserved Domains |
| Program | WWW Address | Program Description |
| DAS | http://www.sbc.su.se/~miklos/DAS/ | Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) |
| HMMTOP | http://www.enzim.hu/hmmtop/ | Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences) |
| PredictProtein | http://dodo.cpmc.columbia.edu/predictprotein/ | Prediction of transmembrane helix location and topology (Columbia University) |
| SOSUI | http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html | SOSUI - Prediction of transmembrane regions (TUAT; Tokyo Univ. of Agriculture & Technology) |
| TMAP | http://www.mbb.ki.se/tmap/ | Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden) |
| TMHMM | http://www.cbs.dtu.dk/services/TMHMM-2.0/ | Prediction of transmembrane helices in proteins (CBS; Denmark) |
| Program | WWW Address | Program Description |
| Coils | http://www.ch.embnet.org/software/COILS_form.html | Prediction of coiled coil regions in proteins. (Lupa method) |
| Paircoil | http://nightingale.lcs.mit.edu/cgi-bin/score | Paircoil - Prediction of coiled coil regions in proteins (Berger's method) |
| Multicoil | http://nightingale.lcs.mit.edu/cgi-bin/multicoil | Prediction of two- and three-stranded coiled coils |
| Program | WWW address | Program Description |
| ProtParam | http://us.expasy.org/tools/protparam.html | Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.) |
| Compute pI/Mw | http://us.expasy.org/tools/pi_tool.html | Compute the theoretical pI and Mw from a SWISS-PROT or TrEMBL entry or for a user sequence |
| MW,pI, Titration | http://www.up.univ-mrs.fr/~wabim/d_abim/compo-p.html | Computes pI, composition and allows to see a titration curve |
| REP | http://www.embl-heidelberg.de/~andrade/papers/rep/search.html | Searches a protein sequence for a repeats |
| SAPS | http://www.isrec.isb-sib.ch/software/SAPS_form.html | Statistical analysis of protein sequences at EMBnet-CH |
| PEST | http://www.icnet.uk/LRITu/projects/pest/ | Identification of PEST regions |
| HLA Bind | http://bimas.dcrt.nih.gov:80/molbio/hla_bind/ | Prediction of MHC type I (HLA) peptide binding |
| SYFPEITHI | http://syfpeithi.bmi-heidelberg.com/scripts/MHCServer.dll/home.htm | Prediction of MHC type I and II peptide binding |
| ProtScale | http://us.expasy.org/cgi-bin/protscale.pl | Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.) |
| Drawhca | http://www.lmcp.jussieu.fr/~soyer/www-hca/hca-form.html | Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence |
| Protein Colourer | http://www2.ebi.ac.uk/cgi-bin/translate/visprot.pl | Tool for colouring amino acid sequence |
| Colorseq | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_color.html | Tool to highlight (in red) a selected set of residues in a protein sequence |
| SMS | http://www.sanbi.ac.za/~rmuller/SMS/index.html | Sequence Manipulation Suite is a collection of web-based programs for analyzing and formatting DNA and protein sequences |
| Program | WWW-Address | Program Description |
| SIM+ LALNVIEW | http://us.expasy.org/tools/sim-prot.html | Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW |
| LALIGN | http://www.ch.embnet.org/software/LALIGN_form.html | Finds multiple matching subsegments in two sequences |
| CLUSTALW | http://www2.ebi.ac.uk/clustalw/ | Multiple Sequence Alignment at EBI |
| T-Coffee | http://www.ch.embnet.org/software/Tcoffee.html | Multiple Sequence Alignment At EMBnet |
| ALIGN | http://www2.igh.cnrs.fr/bin/align-guess.cgi | Multiple Sequence Alignment at Genestream (IGH) |
| DIALIGN | http://bibiserv.techfak.uni-bielefeld.de/dialign/ | Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany |
| Match-Box | http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.shtml | Print-out from multiple alignments University of Namur, Belgium |
| MSA | http://stateslab.bioinformatics.med.umich.edu/ibc/msa.html | Multiple Sequence Alignment at Washington University |
| Multalin | http://prodes.toulouse.inra.fr/multalin/multalin.html | Multiple sequence alignment by Florence Corpet |
| MUSCA | http://cbcsrv.watson.ibm.com/Tmsa.html | Multiple sequence alignment using pattern discovery, at IBM |
| AMAS | http://barton.ebi.ac.uk/servers/amas_server.html | Analyse Multiply Aligned Sequences |
| Bork's alignment tools | http://www.bork.embl-heidelberg.de:8080/Alignment/ | Various tools to enhance the results of multiple alignments (including consensus building) |
| CINEMA | http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2.1/ | Color Interactive Editor for Multiple Alignments |
| ESPript | http://prodes.toulouse.inra.fr/ESPript/cgi-bin/nph-ESPript_exe.cgi | Tool to print a multiple alignment |
| Plogo | http://www.cbs.dtu.dk/gorodkin/appl/plogo.html | Sequence logos at CBS/Denmark |
| JalView | http://www.sander.embl-ebi.ac.uk/Services/protein_profiles/ef-hand-fimb/align.html | Multiple Sequence Alignment Viewer/Editor |
| DbClustal | http://igbmc.u-strasbg.fr:8080/DbClustal/dbclustal.html | Rapid and reliable global multiple alignments of protein sequences detected by database searches |
| Consensus | http://www.bork.embl-heidelberg.de/Alignment/consensus.html | Calculates the consensus for the CLUSTAL or MSF multiple alignment |
| AliBee | http://www.genebee.msu.su/services/malign_reduced.html | Multiple Alignment |
| DiAlign | http://bibiserv.techfak.uni-bielefeld.de/cgi-bin/dialign_submit |
Pairwise and multiple alignments by comparing whole segments of the sequences |
| Multiple Align Show | http://www.bioinformatics.org/SMS/multi_align.html |
Enhance the output of sequence alignment programs |
| ESPrint | http://prodes.toulouse.inra.fr/ESPript/ | Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences |
| Program | WWW-Address | Program Description |
| Phylip | http://bioportal.bic.nus.edu.sg/phylip/index.html | Set of PHYLIP PROGRAMS FOR MOLECULAR SEQUENCE ANALYSIS |
| Phylodendron | http://www.es.embnet.org/Doc/phylodendron/treeprint-form.html | Phylogenetic tree printer - very useful in visualizing *.dnd |
| TreeTop | http://www.genebee.msu.su/services/phtree_reduced.html | Phylogenetic Tree Prediction |
| Program | WWW-Address | Program Description |
| ScanProsite | http://us.expasy.org/tools/scanprosite/ | Scans a sequence against PROSITE or a pattern against SWISS-PROT and TrEMBL |
| InterPro Scan | http://www.ebi.ac.uk/interpro/scan.html | Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases |
| Frame-ProfileScan | http://www.isrec.isb-sib.ch/software/PFRAMESCAN_form.html | Scans a short DNA sequence against protein profile databases (including PROSITE) |
| Pfam-HMM | http://pfam.wustl.edu/hmmsearch.shtml | Scans a sequence against the Pfam protein families db |
| PRATT | http://www2.ebi.ac.uk/pratt/ | Interactively generates conserved patterns from a series of unaligned proteins |
| PPSEARCH | http://www2.ebi.ac.uk/ppsearch/ | Scans a sequence against PROSITE (allows a graphical output); at EBI |
| PROSITE scan | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_prosite.html | Scans a sequence against PROSITE (allows mismatches); at PBIL |
| PATTINPROT | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html | Scans a protein sequence or a protein database for one or several pattern(s); at PBIL |
| SMART | http://smart.embl-heidelberg.de/ | Simple Modular Architecture Research Tool; at EMBL |
| TEIRESIAS | http://cbcsrv.watson.ibm.com/Tspd.html | Generate patterns from a collection of unaligned protein or DNA sequences; at IBM |
| Hits | http://hits.isb-sib.ch/ | Relationships between protein sequences and motifs |
| Program | WWW Address | Program Description |
| AGADIR | http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html | An algorithm to predict the helical content of peptides |
| BCM PSSP | http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html | BCM Protein secondary structure prediction |
| Prof | http://www.aber.ac.uk/~phiwww/prof/ | Cascaded Mutiple Classifiers for Secondary Structure Prediction |
| GOR IV | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html | GOR Secondary Structure Prediction (Garnier et.al.,1996) |
| HNN | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html | Hierarchical Neural Network method (Guermeur, 1997 |
| Jpred | http://jura.ebi.ac.uk:8888/ | A consensus method for protein secondary structure prediction at EBI |
| nnPredict | http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html | University of California at San Francisco (UCSF) |
| PedictProtein | http://cubic.bioc.columbia.edu/predictprotein/ | PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University |
| PREDATOR | http://www.embl-heidelberg.de/cgi/predator_serv.pl | Protein secondary structure prediction from single or multiple sequences at EMBL (Argos' group) |
| ZPRED | http://kestrel.ludwig.ucl.ac.uk/zpred.html | MultPredict Secondary Structure of Multiply Aligned Sequences |
| Program | WWW address | Program Description |
| SWISS-MODEL | http://www.expasy.org/swissmod/SWISS-MODEL.html | An automated knowledge-based protein modelling server |
| Geno3d | http://geno3d-pbil.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home2.html | Automatic modelling of protein three-dimensional structure |
| CPHmodels | http://www.cbs.dtu.dk/services/CPHmodels/ | Automated neural-network based protein modelling server |
| SWEET | http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.html | Constructing 3D models of saccharids from their sequences |
| Mod Web | http://pipe.rockefeller.edu/mwtest-cgi/main.cgi | Server for Comparative Protein Structure Modelling |
| InsightII | http://www.accelrys.com/about/msi.html | Molecular Modelling/Dynamics Tools |
| Sybyl | http://www.tripos.com/software/index.html | Molecular Modelling/Dynamics Tools |
| Modeller | http://guitar.rockefeller.edu/modeller/modeller.html | A program for automated protein homology modeling |
| GROMACS | http://rugmd4.chem.rug.nl/~gmx/ | Complete modelling package for proteins, membrane systems |
| Program | WWW address | Program Description |
| UCLA-DOE | http://fold.doe-mbi.ucla.edu/ | Protein 3D-Structre Prediction Server |
| TOPITS | http://www.embl-heidelberg.de/predictprotein/predictprotein.html | Topology of protein 3D-structure prediction method. |
| 3D-PSSM | http://www.bmm.icnet.uk/~3dpssm/ | Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit) |
| 123D | http://123d.ncifcrf.gov/123D+.html | combines sequence profiles, secondary structure prediction, and contact capacity potentials to thread a protein sequence through the set of structures |
| UCSC HMM Applications | http://www.cse.ucsc.edu/research/compbio/HMM-apps/ | SAM HMM construction and remote homology detection and protein structure prediction |
| FFAS | http://bioinformatics.burnham-inst.org/pages/servers/index.html | Fold assignment method is based on the profile-profile matching algorithm |
| Program | WWW address | Program Description |
| Swiss-PdbViewer | http://us.expasy.org/spdbv/ | A program to display, analyse and superimpose protein 3D structures |
| Mod View | http://guitar.rockefeller.edu/modview/news.shtml | Graphical application for analysis of multiple sequences and structures of biomolecules |
| Rasmol | http://www.umass.edu/microbio/rasmol/ | Molecular Visualization Freeware |
| PREPI | http://www.bmm.icnet.uk/people/suhail/prepi.html | Molecular Graphics Program |
| SURFNET | http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html | Generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file |
| Raster3D | http://www.bmsc.washington.edu/raster3d/raster3d.html | Set of tools for generating high quality raster images of proteins or other molecules |
| WHAT_CHECK | http://www.cmbi.kun.nl/swift/whatcheck/ | The protein verification tools from the WHAT IF program |
| Procheck | http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html | A program that checks the stereo-chemical quality of a protein structure |
| WebMol | http://www.cmpharm.ucsf.edu/~walther/webmol.html | A Java Protein Structure Viewer |
| VMD | http://www.ks.uiuc.edu/Research/vmd/ | VMD (Visual Molecular Dynamics) |
| WinMGM | http://www.ibanez.li/~mr/index.html | A molecular graphics program for PDB files that runs on Linux intel and solaris intel platforms |
| Swiss-PDB Viewer | http://www.expasy.ch/spdbv/ | A 3D graphics and molecular modeling program for the simultaneous analysis |
| PyMOL | http://pymol.sourceforge.net/ | A free and open-source molecular graphics system for visualization |
| MolScript | http://www.avatar.se/molscript/ | A program for displaying structures in both detailed and schematic formats and writing images in various formats |
| PyMOL | http://pymol.sourceforge.net/ | A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. |
| Qmol | http://lancelot.bio.cornell.edu/jason/qmol.html | A lightweight OpenGL based molecular viewer for Windows95/NT/00 and X Windows |
| MidasPlus | http://www.cgl.ucsf.edu/Outreach/midasplus/ | A program for displaying, manipulating and analysing?macromolecules |
| GRASS | http://trantor.bioc.columbia.edu/GRASS/surfserv_enter.cgi | Graphical Representation and Analysis of Structure Server |
| Program | WWW-Address | Description |
| AbM | http://www.accelrys.com/about/oxmol.html | Antibody Structure Modeling - Oxford Molecular Group, Inc. |
| AMBER | http://www.amber.ucsf.edu/amber/amber.html | AMBER - Oxford Molecular Group, Inc. |
| AMPAC | http://www.semichem.com/ampac.html | Graphical User Interface |
| AutoDock | http://www.scripps.edu/pub/olson-web/doc/autodock/ | Automated Docking of Flexible Ligands to Macromolecules - Scripps Research Inst |
| CAChe | http://www.accelrys.com/about/oxmol.html | Oxford Molecular Group, Inc. |
| CAVEAT | http://www.cchem.berkeley.edu/~pabgrp/Data/caveat.html | Design of Organic Molecules |
| Cerius2 Visualizer | http://www.accelrys.com/about/msi.html | Molecular Simulations, Inc. |
| CHIME | http://www.mdlchime.com/chime/ | CHIME - MDL Information Systems, Inc. |
| GLOCP | http://clogp.pomona.edu/chem/biobyte/manuals/ClogP_Formatted.html | Quantitative Structure Activity Relationships (QSAR) |
| CloneMap | http://www.cgcsci.com/#CloneMap | Plasmid map drawing, restriction site mapping, and virtual cloning -CGC Scientific, Inc. |
| Cobra | http://www.accelrys.com/about/oxmol.html | Oxford Molecular Group, Inc. |
| Composer | http://www.tripos.com/software/composer.html | Complete, Accurate Protein Homology Models-Tripos, Inc. |
| CONCORD | http://www.tripos.com/software/concord.html | Fast, High Quality 3D Structures from 2D Input -Tripos, Inc. |
| DISCO | http://www.tripos.com/software/disco.html | Rapid, Intelligent Pharmacophore Generation -Tripos, Inc. |
| DIVA | http://www.accelrys.com/about/oxmol.html | Oxford Molecular |
| AutoDock3.0 | http://www.scripps.edu/pub/olson-web/dock/autodock/ | A suite of automated docking tools. |
| DOCK | http://www.cmpharm.ucsf.edu/kuntz/dock.html | Docking Program |
| FlexiDock | http://www.tripos.com/software/fdock.html | Drug Design Tripos, Inc. |
| GASP | http://www.tripos.com/software/gasp.html | Automatic pharmacophore elucidation with full Conformational flexibility |
| GRAMM | http://reco3.ams.sunysb.edu/gramm/ | Protein Docking |
| QUANTA | http://www.accelrys.com/about/msi.html | Molecular Simulations Inc., (Burlington, MA, USA) |
| FTDOCK | http://www.bmm.icnet.uk/docking/ | A program for carrying out rigid-body docking between biomolecules |
| ECEPPAK | http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/ | Cornell Theory Center package to carry out global conformational searches using the ECEPP/3 force field |
| CHARMM | http://yuri.harvard.edu/ | (Chemistry at HARvard Molecular Mechanics) is a molecular dynamics and energy minimization program |
| ICM | http://www.molsoft.com/icmpages/icmcore.htm | MolSoft ICM programs and modules for applications including for structure analysis, modeling, docking, homology modeling and virtual ligand screening |
| LOOPP | http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/ | Linear Optimization of Protein Potentials. Cornell Theory Center program for potential optimization and alignments of sequences and structures |
| MOIL | http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/ | Cornell Theory Center package for molecular dynamics simulation of biological molecules |
| NAMD | http://www.ks.uiuc.edu/Research/namd/ | A parallel object-oriented molecular dynamics simulation program |
| WAM - Web | http://antibody.bath.ac.uk/ | Antibody Modelling |
| CastP | http://cast.engr.uic.edu/cast/ | Server that calculates measurements of structural pockets and cavities of proteins and nucleic acids |
| Efsite | http://pi.protein.osaka-u.ac.jp/eF-site/ | eFsite (electrostatic-surface of Functional site) |
| PASS | http://www.delanet.com/~bradygp/pass/ | Putative Active Site with Spheres (Freeware) |