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Proteases
Sequence Databases
Structure Databases
Bibliography
Genomes
Sequence Analysis
Structure Analysis
Journals
Gen.Projects
Phylogeny
Structure Predictions
Research Inst.
Functions
Mutations
Organizations
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The purple buttons in the menu above are short cuts to the descriptive menu below.
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Web sites about proteases

  horiz_blue.gif International Proteolysis Society : meetings - contacts
  MEROPS : The Peptidase Database - Babraham Institute, Cambridge (UK)
  Proteases/ExPASy :Classification of peptidases and links to SWISS-PROT - The Swiss Institute of Bioinformatic
  Prolysis :A protease and protease inhibitor Web server - Universite de Tours (France)
  HIV protease database : National Cancer Institute - Frederick Cancer Research and Development Center (USA)
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Huge updated lists of links toward web sites about molecular biology, biochemistry and biophysics:
Amos Bairoch
, MCB Harvard

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Sequence Databases

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DNA>P Genetic code viewer at EBI
All Sequence Retrieval System: Network Browser for Databanks in Molecular Biology (ExPASy, Swiss)
  and mirrors ( I.Pasteur-France,)
DNA EMBL: EMBL Nucleotide Sequence Database
DNA Genbank: NIH DNA sequence database
DNA Imgt: ImMunoGeneTics database
DNA Nmuc: Non redundant Genbank+Embl
DNA Vector: vector subset of GenBank(R) assembled by NCBI staff
DNA GeneCards: human genes, proteins and diseases
Prot Genpept: Translations of Genbank
Prot Nrl3d: Sequence and annotation informations extracted from PDB
Prot Nrprot: Non redundant Swissprot, Genpept, Pir, Nrl3d
Prot Owl: Composite Protein Sequence Database
Prot PIR: Protein Information Resource, Blast PIR, (code identifier at PIR)
Prot Sbase: A Collection of Annotated Protein Domain Sequences
Prot SwissProt: Annotated protein sequence database - The Swiss Institute of Bioinformatic (SIB/ExPASy)
Prot TrlEMBL & New-TrlEMBL: Translation of EMBL not in SwissProt at SIB/ExPASy
Prot Kabat: Proteins of Immunological Interest
Prot Complete genome PIR database
Enzyme Enzyme Nomenclature Database (ExPASy - Swiss) EC entries
Enzyme Biochemical Pathways (ExPASy - Swiss)
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Genome Databases

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DNA List of the completed genomes at PIR at NBRF.
DNA Classified microbial genomes and taxonomy at NCBI
DNA List of the completed genomes of microorganisms at Infobiogen and Blast or FastA them.
DNA List of the incompleted genomes of microorganisms at Infobiogen and Blast or FastA them.
DNA List of 8 complete genomes (COGs) at NCBI and Blast them.
DNA E.coli : complete genome, Colibri: relational database, Entrez & Blast at NCBI
DNA M.tuberculosis : complete genome
DNA H.pylori :complete genome , Entrez & Blast NCBI
DNA Yeast : chromosomes , (Yeast Proteome Database), Entrez at NCBI, GeneQuiz at EBI
DNA Arabidopsis thaliana : genome, BLAST at WU
DNA C.elegans: complete genome, BLAST at WU
DNA C.briggsae: complete genome, BLAST at WU
DNA B.subtilis : complete genome, Subtilist: relational database
DNA Haemophilus influenzae: complete genome, Entrez & Blast at NCBI, GeneQuiz at EBI
DNA Human: chromosomes in progress, BLAST on human genome
DNA Mycoplasma genitalium : complete genome, Entrez & Blast at NCBI, GeneQuiz at EBI
DNA Mycoplasma pneumoniae: complete genome, Entrez & Blast at NCBI
DNA Synechocystis: complete genome (cyanobacteria), Entrez & Blast at NCBI
DNA Methanococcus jannaschii : complete genome , Entrez & Blast at NCBI, GeneQuiz at EBI
DNA Parasites genomes : Blast parasites at EBI
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Genome Projects

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  Argonne National Laboratory (USA)
  Genome Sequencing Center WUSTL (USA)
  TIGR (USA)
  Genoscope (France)
  Sanger Center : sequencing center list, snapshot of genome projects (UK)
  Human Genome Center: Institute of Medical Science University of Tokyo (Japan).
  CLUE : collection of convenient links about genetic research (Japan).
  GÉNÉTHON : Human Genome Research Centre (France)
  GDB : The genome database
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Sequence Analysis

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DNA>P Protein Engine : Translate DNA sequences at EBI
Any GQserve: from GeneQuiz, highly automated analysis of biological sequences at EBI
Any BLAST , WU-BLAST, PHI-BLAST, PSI-BLAST at NCBI (mirror I.Pasteur , ISREC, Blast2 and WUBlast2 at EBI, WUBlast2 at EMBL)
Any FASTA,TFASTA : Search in database by sequence alignment (mirror I.Pasteur , Fasta3 at EBI)
Any Scanps : Fast Smith & Waterman at EBI
Any Ssearch3 : Smith & Waterman at EBI
Any FASTA,TFASTA : (mirror I.Pasteur )
Any CINEMA v2.1: Colour INteractive Editor for Multiple Alignments
Any Clustalw : Multiple Alignements , (mirror I.Pasteur, EBI, PIR)
Prot BLITZ : electronic mail server for MPsrch
Prot EBI Biocatalog: catalog of softwares about sequence analysis
Prot BCM : Integrated interface for various molecular biology search and analysis
Prot Prosite : Dictionary of Protein Sites and Patterns
Prot ProDom: Homologous domains from Swiss-Prot, from complete genome, Blast ProDom on genomes
Prot BCM Search Launcher: Multiple Sequence Alignments
Prot PFam: Protein Domain Families, (mirror WUSTL)
Prot Blocks: Most highly conserved region of proteins without gap
Prot Prints: Protein Motif Fingerprint Database
Prot Prosearch: search Prosite patterns in a sequence
Prot Cognitor: compare your protein sequence to 8 complete genome, look for ortholog groups (NCBI)
Prot Ppsearch : Protein motifs or fingerprint searches at EBI
Prot Pratt : Protein motif or fingerprint discovery at EBI
Prot SAPS : Statistical Analysis of Protein Sequences at EBI
Prot Protein Annotator Assistant : hypothesise the function(s) of a protein sequence at EBI
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Phylogeny

  horiz_blue.gif Phylip : Phylogeny Inference Package programs (mirror Institut Pasteur, Protdist, Protpars, Fitch, Kitsch other mirrors SPR Institute, Singapore Univ., Wistar Institute)
  Compare 3.0: Computer programs for the phylogenetic analysis of comparative data
  Tree of Life :Information about phylogeny and biodiversity
  TreeBASE: A database of phylogenetic trees and data matrices published in the primary systematic literature.
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Structure Predictions

Prot>2D horiz_blue.gif Predator: Protein secondary structure prediction from a single sequence or a set of sequences
Prot>2D NNSSP: Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignment
Prot>2D JPred : A consensus method for protein secondary structure prediction at EBI
Prot>2D Bio-lirmm : Protein secondary structure prediction and global multiple alignment
3D>3D Confmat : Side chain packing optimization on a given main chain template for protein
Prot>3D Homology : SCMF Homology Modelling Program
Prot>3D Swiss-Model : An Automated Comparative Protein Modelling Server
Prot>3D Homology : SCMF Homology Modelling Program
Prot>3D Homology : SCMF Homology Modelling Program
Prot>3D EBI BioCatalog: catalog of softwares about structure prediction
Prot>3D The PredictProtein server and METAPP : at EBI
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Structure Databases

  horiz_blue.gif Protein Databank : Structure coordinates from RCSB and mirrors Rutgers, SDSC and NIST or list.
  HIV protease database : National Cancer Institute - Frederick Cancer Research and Development Center (USA)
  BioMagResBank(BMRB): A repository for data from NMR spectroscopy on proteins and peptides.
  PQS Protein Quaternary Structure Query Form at the EBI
  Atlas of Protein Side-Chain Interactions :
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Structure Analysis

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  SCOP : Structural Classification Of Proteins and mirrors. BLAST on SCOP
  CATH : Protein Structure Classification
  HSSP :Homology-derived secondary structure of proteins
  WALI: a SESAM Structure Database interface
  Stride : Protein secondary structure assignment from atomic coordinates
  DSSP: Definition of secondary structure of proteins given a set of 3D coordinates
  DSC : Discrimination of protein Secondary structure Class
  Environ : calculate accessible as well and buried surface area in protein structure
  CSR : Maximal Common 3D Substructure Searching
  EBI,Biocatalog: catalog of softwares about structure analysis
  MaxSprout : generating protein backbone and side chain co-ordinates from a C(alpha) trace (EBI)
  TOPS : protein structural topology and protein topology cartoons (EBI)
  3 Dee : Database of Protein Domain Definitions (EBI)
  STRUDL: an automatic procedure for identifying domains from protein atomic coordinates.
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Mutations

  horiz_blue.gif GENLINE : electronic clinical genetics knowledge base
  vWF Database : point mutations, insertions, deletions, and polymorphisms found in von Willebrand Factor
  Mutation Database Web Site : HUGO mutation database initiative.
  Mutability: Check mutability from dna sequences (EBI)
  DNA mutation checker : (EBI)
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Fonctions

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  Protein Annotator Assistant : hypothesise the function(s) of a protein sequence at EBI
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Scientific Organizations

  horiz_blue.gif International Proteolysis Society : meetings - contacts
  Protein Society: meetings - contacts
  American Society for Biochemistry and Molecular Biology : meetings - contacts
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Universities, Institutes, Fundations

  horiz_blue.gif Institut Pasteur (Paris, France)
  Washington University (St Louis, USA)
  Search in Universities
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Pharmaceutical companies horiz_blue.gif

  Abbott Laboratories Organon
  Akzo Nobel Pharmaceutical Companies
  Astra Pfizer
  Bristol-Myers Squibb Pierre Fabre
  Ciba Pharmacia & Upjohn, Inc
  Knoll Roche
  Eli Lilly Rotta Research Laboratorium
  Glaxo Wellcome Sankyo Pharma GmbH
  Hoechst Sanofi
  Johnson & Johnson Schering Plough
  Merck & Co., Inc. SmithKline Beecham
  Merck KGaA Darmasadt Solvay S.A.
  Monsanto Business Units - Searle Synthelabo
  NeuroSearch A/S Warner-Lambert
  Newspage U.S. Pharmaceutical Industry Zeneca
  Novartis  
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Bioinformatic companies (to the Amos Bairoch's list)

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Bibliography

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  PubMed: Medline at the National Library of Medicine
  Ovid on the Becker Library, personal account requested (WUStL-Sc.Med)
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Journals, Reports, Reviews

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  Cell : (mirrors)
  EMBO Journal : published for the European Molecular Biology Organization (mirrors)
  Journal of Biological Chemistry : published by Am.Soc.Biochem.Mol.Bio. (mirrors)
  Journal of Molecular Biology :
  Nature : International weekly journal of science
  Proceedings of the National Academy of Sciences of USA . (mirrors)
  Science : Published by the Am. Asso. for the Advancement of Science (mirror)
  Links to most of the Journal web sites at the National Library of Medicine
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Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
Saint Louis, MO, U.S.A.

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