Contents:

Databases
Sequence analysis
Structure classification and analysis
Structural genomics
Structure verification
Organisations
Lists of resources
Other WWW servers

Other Information Sources:

General Information
Software
Related News Groups
Education

Additional resources may be found in the CMS Molecular Biology Resource

Databases

• ABG: Directory of 3D structures of antibodies 
• BioBase
  The Danish Biotechnological Database 
• BMCD
  Biological Macromolecule Crystallization 
• BioImage
  Multidimensional Biological Images (EM) 
• BMRB
  BioMagResBank (NMR) 
• CAZy
  Carbohydrate-Active enZYmes 
• CCDC
  Cambridge Crystallographic Data Centre (small molecules) 
• ENZYME
  Enzyme Nomenclature 
• Entrez
  NCBI databases 
• ExPASy
  Molecular Biology server 
• GeneCards
  Database on human genes, proteins and diseases 
• GDB
  Genome Data Base 
• GenBank
  Nucleotide sequences 
• HIV Protease Database 
• IMGT
  International ImMunoGeneTics Database 
• Klotho
  Biochemical Compounds Declarative Database 
• LIPIDAT
  Lipid mesophase and crystal polymorphic transitions 
• MacroMolecular Assemblies, EBI
  Coordinates for probable protein quaternary structures 

• MEROPS
  Peptidase Database 
• Metalloprotein Database and Browser 
• ModBase
  A database of comparative protein structure models 
• NDB
  Nucleic Acid Database 
• PDB RCSB PDB in RCSB site
• PDB 3DB Browser
  Interface to the PDB available at most former BNL PDB mirror sites
• PDBLite
  Simple PDB search for students and educators 
• PDBOBS
  Archive of obsolete PDB entries 
• PDB at a Glance
  Classification of the structures in the PDB 
• PIR
  Protein Information Resource 
• Prolysis
  Proteases and protease inhibitors 
• Promise
  The Prosthetic groups and Metal Ions in Protein Active Sites Database 
• Protein Kinase Resource 
• Protein Motions Database 
• RELIBase
  Structural data about receptor/ligand complexes (UK), mirrored in USA
• SWISS-PROT
  Protein Sequence Database 
• SWISS-MODEL Repository (3DCrunch)
  A protein model database 
• Vitamin D Nuclear Receptor Site 

Sequence analysis

• BLAST
  Basic Local Alignment Tool with interfaces at BCM(USA), GeneStreamCRBM(France), DDBJ(Japan), DISC/AFFRC(Japan), EERIE-GeneStream(France), EERIE-GenQuest(France), EMBL(Germany), EPFL(Switzerland), ExPasy(Switzerland), GenomeNet(Japan), ISREC(Switzerland), NCBI(USA), ORNL(USA), Pasteur Inst(France), Stanford University(USA)
• EMBL (SRS)
  EMBL Sequence Retrieval System 
• FASTA
  Implementations of FASTA (Pearson and Lipman) sequence alignment method at DISC/AFFRC(Japan), EBI(UK), GenomeNet(Japan), EERIE-GeneStream(France), EERIE-GenQuest(France), EMBL-Heidelberg(Germany), ICBP(France), IUBio(USA), JHU(USA), MIPS(Germany), ORNL(USA), Pasteur Inst(France), Stanford University(USA)

• Human Genome Project Information 
• PROSITE
  Detection of sequence patterns with interfaces at GenomeNet(Japan), EBI(UK), EERIE(France), ISREC(Switzerland), EMBNET(Switzerland), ExPasy(Switzerland)
• Smith-Waterman
  Implementations of Smith-Waterman sequence alignment at SW-MPsrch-PP/PPA DISC/AFFRC(Japan), SW-SSEARCH EERIE(France), SW-SSEARCH CRBM(France), SW-FDF Stanford U(USA), SW-FDF EMBNet(Switzerland), SW-GenQuest EERIE(France), SW-GenQuest ORNL(USA), SW-BIC EBI(UK), SW-GenWeb Weizmann Inst(Israel)

Structure classification and analysis

• CATH
  Class, architecture, topology and homologous superfamily 
• CE/CL
  Alignment server and databases for structure comparison by Combinatorial Extension (CE) and Compound Likeness (CL) 
• COMPASS
  CAMbridge database of Protein Alignments organised as Structural Superfamilies 
• Culled PDB
  Representative PDB structures 
• DALI
  Comparison of protein structures in 3D 
• DSMP
  Dictionary of Structural Motifs in Proteins, based on analysis of proteins in PDB_Select 
• GRASS
  Graphical Representation and Analysis of Structure Server 
• HIC-Up
  Hetero-compound Information 
• HOMSTRAD
  Homologous Structure Alignment Database 
• IMB Jena Image Library of Biological Macromolecules 
• Library of Protein Family Cores 
• Ligand-Protein Contacts and Contacts of Structural Units
  A resource which provides an analysis of interatomic contacts in ligand-protein complexes (LPC) or an analysis of interatomic contacts in protein entries (CSU) 
• Macromolecular Structures Database 

• Molecules R Us 
• MOOSE
  Macromolecular Structure Query 
• NMR model representative structure 
• NRL_3D
  Sequence-Structure Database produced by PIR 
• OLDERADO
  On Line Database of Ensemble Representative And DOmains 
• PDB_Select
  Representative PDB structures 
• PDBSum
  Summaries and structural analyses of PDB data files 
• SCOP
  Structural Classification of Proteins (UK), mirrored around the world
• Protein Sidechain Webpage
  Information on sidechain conformational analysis, sidechain rotamer libraries, and sidechain conformation prediction 
• STING
  Sequence To and withIN Graphics (USA), mirrored in Israel
• SPIN-PP
  Surface Properties of Interfaces - Protein Protein interfaces 
• SWISS-MODEL
  A server for automated protein modeling 
• TOPS - Protein Topology 
• Uppsala Electron Density Server 

Structural genomics

• NIH structural genomics resource 

• Stanford structural genomics resource 

Structure verification

• Biotech Validation Suite (Germany), mirrored in UK 
• ERRAT Structure Submission Page 

• Verify3D Structure Evaluation Server 

Organisations

• ACA
  American Crystallographic Association 
• Biophysical Society 
• DOE
  United State Department of Energy 
• EBI
  European Bioinformatics Institute 
• EMBL
  European Molecular Biology Laboratory (Heidelberg) 
• IUCr
  International Union of Crystallography 
• NBIF
  National Biotechnology Information Facility 

• NBRF
  National Biomedical Research Foundation 
• NCBI
  National Center for Biotechnology Information 
• NIH
  National Institutes of Health 
• NSF
  National Science Foundation 
• SDSC
  San Diego Supercomputer Center 
• Weizmann Institute, Genome and Bioinformatics 

Lists of resources

• A Collection of WWW Links to Information and Services Useful to Molecular Biologists
  Pedro's BioMolecular Research Tools 
• BioSites
  Virtual Catalog of Selected Internet Resources in the Biomedical Sciences 
• Crystallography World Wide 
• Computational Molecular Biology at NIH 

• Genamics SoftwareSeek
  Collection of molecular biology and biochemistry tools 
• HighWire Press
  Stanford University's collection of journals 
• Resource for Macromolecular Structure Information 
• Web Resources for Protein Scientists
  Protein Society 

Other WWW servers

• Biomolecular Modelling Laboratory 
• IUCr Crystallography Computing School 
• Synchrotron Beamlines for Macromolecular Crystallography
  BioSync group resource containing information for prospective synchrotron users in the field of macromolecular crystallography