| Baylor College |
Baylor College of Medicine, Houston, Texas, USA |
| Beijing HGC |
Beijing Human Genome Center, Institute of Genetics, Chinese Academy
of Sciences, Beijing, China |
| Braunschweig GBF |
Gesellschaft für Biotechnologische Forschung mbH, Braunschweig,
Germany |
| Genoscope |
Genoscope, Evry, France |
| Waltham GTC |
Genome Therapeutics Corporation, Waltham, MA, USA |
| Jena IMB |
Institute for Molecular Biotechnology, Jena, Germany |
| Joint Genome |
Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA,
USA |
| Keio University |
Keio University, Tokyo, Japan |
| Max Planck |
Max Planck Institute for Molecular Genetics, Berlin, Germany |
| RIKEN |
RIKEN Genomic Sciences Center, Saitama, Japan |
| The Sanger Centre |
The Sanger Centre, Hinxton, U.K. |
| Stanford TDC |
Stanford DNA Sequencing and Technology Development Center, Palo Alto,
CA, USA |
| Washington Univ. Genome
Center |
University of Washington Genome Center, Seattle, WA, USA |
| Washington Univ.
Mult. Seq. Center |
University of Washington Multimegabase Sequencing Center, Seattle,
WA,USA |
| Whitehead Institute |
Whitehead Institute for Biomedical Research, MIT, Cambridge, MA, USA |
| Washington Univ. Genome Seq.
Center |
Washington University Genome Sequencing Center, St. Louis, MO, USA |
| ClustalW_EMBL |
CLUSTAL W (1.75) Multiple Sequence Alignments (EMBL-ES) |
| ClustalW_EBI |
ClustalW Server at EBI |
| ClustalW_BioWeb |
ClustalW Server at the Institut Pasteur (France) |
| T-COFFEE |
T-Coffee: Accurate, but slow, Multiple Sequence Alignment server (EMBNET.CH)
(limit: 30 seq, 1000 res) |
| T-COFFEE |
T-Coffee: Cedric Notredame page (University of Nijmegen, NL)
(limit: 20 seq 300 res) |
| CMBI_Tree_Plot |
CMBI Phylogenetic Tree Plot Server (University of Nijmegen, NL) (GIF,
PS,.. trees) |
| Phylodendron |
Phylodendron: Phylogenetic tree printer (EMBL-ES) |
| PHYLIP |
PHYLIP is a free package of programs for inferring phylogenies (Whasington
Univ.) |
| WebPHYLIP |
WebPHYLIP is a web version of the original PHYLIP package. National
University of Singapore. |
| BioWebPHILIP |
PHILIP (web version) at the Institut Pasteur (France) |
| PAUP |
PAUP is a software package for inference of evolutionary trees (Florida
Stat. Univ.) |
| Philogeny
Programs |
Here are some 193 of the phylogeny packages, and 16 free servers. |
| Phylogeny Course |
Molecular Systematics and Evolution Course (London - Rio de Janeiro) |
| Prosite |
ProfileScan Server (ISREC, CH) |
| ProDom |
ProDom protein domain database (INRA, FR) |
| InterPro |
Integrated resource of protein domains and functional sites. (EBI,
UK) |
| PFAM |
Protein families database of alignments and HMMs (Sanger, UK) |
| DART |
Domain Architecture Retrieval Tool (It shows similar domain achitectures,
too) (NCBI) |
| PRINTS |
Protein Motif Fingerprint Database (UCL, UK) |
| SMART |
Simple Modular Architecture Research Tool. Domains/motif detection
(EMBL) |
| Blocks/Prints |
Searching both Blocks+ and Prints databases (FHCRC, USA) |
| SignalP |
Predicts the presence and location of signal peptide (CBS, DK) |
| TMHMM |
Prediction of transmembrane helices in proteins (CBS, DK) |
| HMMTOP |
Prediction of transmembrane helices and topology of proteins (Inst.
Enzymol. Budapest) |
| SignalP |
Predicts the presence and location of signal peptide (CBS, DK) |
| COILS |
Prediction of Coiled Coil Regions in Proteins (ISREC, CH) |
| MultiCoil |
Program for Predicting Two- and Three-Stranded Coiled Coils (MIT, USA) |
| Jpred |
A consensus method for protein secondary structure prediction (EBI,
UK) |
| Psi-Pred |
Protein structure prediction server (secondary structure &
transmembrane topology) (University College London, UK) |
| APSSP |
APSSP: Advanced Protein Secondary Structure Prediction Server (Chandigarh,
INDIA) |
| TOPS |
Protein Topology Home Page (EBI, UK) |
| SAM-T99 |
SAM-T99 secondary structure prediction. |
| Swiss-Model |
SWISS-MODEL. An Automated Comparative Protein Modelling Server (ExPASy,
CH) |
| SWISS-MODEL
Repository |
SWISS-MODEL Repository. A database for theoretical protein models (ExPASy,
CH) |
| WHATIF |
WHAT IF Web interface: homology modelling, drug docking,
electrostatics calculations, structure validation and visualisation. |
| TITO/Modeller |
Modeller at the CBS Bioinformatic Tools Server (Montpellier, France) |
| CPHmodels |
The CPHmodels Server using comparative (homology) modelling (BioCentrum,
Denmark) |
| SDSC1 |
"SDSC1" - SDSC Protein Structure Homology Modeling Server (San Diego,
USA) |
| PredictProtein |
The PredictProtein server (TOPITS) (Columbia, USA) |
| PredictProtein
(local) |
The PredictProtein server (TOPITS) (EMBnet / CNB, ES) |
| 3D-PSSM |
3D-PSSM Protein Fold Recognition (Threading) Server (Imperial Cancer
Res. Fund., UK) |
| UCLA-DOE |
UCLA-DOE Fold-Recognition server (UCLA, USA) |
| Psi-Pred (GenThreader) |
Protein structure prediction server (sequence profile based fold
recognition) (University College London UK) |
| SAM-T99 |
SAM-T99 protein structure HMM library search. |
| FFAS |
Fold & Function Assignment System. (Burnham Institute, USA) |
| Fold-Pred |
Protein Fold Prediction in the context of SCOP. |
| FUGUE |
FUGUE Profile Library Search Against HOMSTRAD (Cambridge, UK) |
| Threading
Meta-Server |
Threading Meta-Server at the CBS Bioinformatic Tools Server (Montpellier,
France) |
| Threading
Meta-Server |
Threading Meta-Server at BioInfo.PL (Warszawa, Poland) |
| SAUSAGE |
SAUSAGE: Protein threading with flexible force fields (Canberra,
Australia) |
| LOOPP |
A program for potential optimization and alignments (Cornell, USA) |
| Superfamily |
HMM library and genome assignments server (Cambridge, UK) |
| PDB - EBI |
Protein Data Bank (EBI) |
| PDB - RCSB |
Protein Data Bank (RCSB) |
| PDBsum |
Summaries and structural analyses of PDB data files (UCL, UK) |
| Get ExPDB |
Get ExPDB entries for a PDB code (Swiss-Model, ExPASy, CH) |
| OCA |
PDB advanced browser(EBI) |
| PDBselect |
Subset of the structures in the PDB that does not contain (highly)
homolog sequences |
| EC->PDB |
Enzyme Structures deposited in PDB (UCL, UK) |
| Prosite->PDB |
PROSITE patterns in PDB entries (UCL, UK) |
| Ligands->PDB |
List of ligands bound to PDB srtuctures (UCL, UK) |
| RELIBASE |
Relibase: A program for searching protein-ligand databases. |
| Molecular
Models |
1400 Molecular Models (from chemistry) in .pdb format (Okanagan University
College, Canada) |
| NDB |
The Nucleic Acid Database Project (UK) (Nucleic Acid Structures) |
| IMB Jena |
IMB Jena Image Library of Biological Macromolecules (Jena, Germany) |
| SCOP |
Structural Classification of Proteins (MRC-LMB, UK) |
| CATH |
CATH Protein Structure Classification (UCL-BSM, UK) |
| The Dali server |
The Dali server: Network service for comparing protein (query) structures
in 3D (EBI) |
| WWWSUP |
Pairwise Superposition of Protein 3D Structures (CIGB, Habana, Cuba) |
| FSSP |
Fold classification based on Structure-Structure alignment of Proteins
(FSSP) (EBI) |
| DaliDD |
Dali Domain Dictionary: structural classification of protein domains
(EBI) |
| Homstrad |
Homologous Structure Alignment Database (CrystBioc, UK) |
| 3Dee |
3 Dee - A Database of Protein Domain Definitions (EBI) |
| CAMPASS |
CAMbridge database of Protein Alignments organised as Structural Superfamilies
(CrystBioc, UK) |
| ProSup |
Structure Comparison Server (Manfred J. Sippl - CAME) |
