Practical "Structural Databases" - EMBO Bioinformatics Course

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Primary structural databases
- Protein Data Bank in Europe (PDBe)
- Protein Data Bank at RCSB
- Nucleic Acid Database (Rutgers)
- PDBOBS at SDSC (archive of obsolete PDB entries)
- Beta-release of the RCSB Protein Data Bank (mostly for expert-users)
- SeqAlert (alerts you when a structure has been deposited that displays homology to a sequence you are interested in; Weizmann)
- PDB current holdings
- PDB Newsletter archive (dating back to September 1974 !)
Front-ends to the structural databases
- SearchLite (PDB)
- SearchFields (PDB)
- PDBsum (EBI; new site !)
- PDBsum (UCL; old site !)
- PDB Lite (list of OCA sites)
- Entrez-Structure (NCBI)
- MMDB, Molecular Modelling DataBase (NCBI)
- BioMolQuest (Buffalo)
- IMB Search (Jena)
- PDB at a Glance (NIH)
- PDBFINDER (CMBI)
- SRS 3D (EBI)
- SRS6 (EBI)
- SRS5 (EMBL)
Experimental data
- BioMagResBank (NMR data; Wisconsin)
- HAD, Heavy-Atom Databank (heavy-atom derivatives)
- BMCD (crystallisation conditions; NIST)
- EDS (Electron Density Server; Uppsala)
Visualisation
- Molecules R US (NIH)
- SWISS-3DIMAGE (ExPASy)
- Image Library of Biological Macromolecules (IMB Jena)
- Biochemistry Graphics on the Web (CMU)
- GRASS (Graphical Representation and Analysis of Structure Server; Columbia)
- STING (Sequence To and withIN Graphics; Columbia)
- Molecular Graphics Art Shows (Scripps)
Visualisation software
- MolVisIndex (World Index of Molecular Visualization Resources)
- Freely available molecular visualisation programs
- Astex Viewer (Astex Technology)
- Rasmol (Bernstein)
- Rasmol (UMass)
- Chime (MDL)
- Deep View Swiss-PdbViewer (Expasy)
- MolScript (Kraulis)
- MolMol (ETH)
- ModView (UCSF)
- Mage (Duke)
- Protein Explorer (UMass)
- WebMol (Java-based viewer; UCSF)
- PyMOL
- LIGPLOT (UCL)
- Garlic (Croatia)
- Indie - Molecular Movies (server at NIH)
- Indie - Morph a Molecule (server at NIH)
- TopDraw (program to create your own topology drawings; Dundee)
- RbDe (residue-based diagram editor; Cornell)
Structural macro-analysis (folds, classification, similarity, sequence alignments)
- CATH (classification database; UCL)
- CATH PFDB (protein family database; UCL)
- SCOP (classification database; MRC-LMB)
- FSSP (Fold classification based on Structure-Structure alignment of Proteins; EBI)
- TOPS (protein topology database; Leeds)
- TOPS (protein topology database; EBI)
- CE similarity database and server (SDSC)
- Dali similarity server (EBI)
- DEJAVU similarity server (Uppsala)
- MATRAS server (Japan)
- PRIDE server (Trieste)
- SSM server (EBI)
- TOP server (Lund)
- TOPS server (EBI)
- TOPSCAN server (Reading)
- VAST similarity database and server (NCBI)
- DBAli, DataBase of sequence and structure Alignments (UCSF)
- PALI, Phylogeny and ALIgnment of homologous protein structures
- Guoguang Lu's programs and servers (Lund)
- STRUCTAL server (superimposing two structures; Yale)
- SSAP server (superimposing two structures; UCL)
- K2 server (superimposing two structures; Boston)
- BioInfo3D (servers for superimposing two or more structures; Tel Aviv)
- DynDom server (analyses conformational difference between two proteins; Norwich)
- eF-site (electrostatic surfaces; Osaka)
- ESPript/ENDscript (annotating structures; Toulouse)
Structural micro-analysis (sites, small motifs, waters)
- SPASM server (3D-motif recognition; Uppsala)
- PINTS server (Patterns in Non-homologous Tertiary Structure; Heidelberg)
- PINTS Weekly (Heidelberg)
- SuMo server (3D-motif recognition; Lyon)
- CSA (Catalytic Site Atlas; EBI)
- PROCAT (UCL)
- DSMP (Database of Structural Motifs in Proteins; CDFD, India)
- Site Database (Jena)
- SURFACE (Functional surface patches; Rome)
- WAP, Water Analysis Package (Bangalore)
- PROSITE patterns in PDB entries (EBI; new site)
- 3MOTIF (find sequence motifs in structures; Stanford)
- WebFEATURE (find functional sites in structures; Stanford)
- Motif3D (find sequence motifs in structures; Manchester)
- NCI (non-canonical interactions; Cambridge)
Model validation
- PDBReport (CMBI)
- Biotech validation server (EBI)
- Biotech validation server (EMBL)
- ADIT server (PDB)
- DRESS (re-refined NMR structures; CMBI)
- ERRAT server (UCLA)
- Verify3D server (UCLA)
- MolProbity server (Duke)
- RamPage server (Cambridge)
- VADAR server (Alberta, Canada)
- PARVATI server (Washington)
- ANOLEA server (Atomic Non-Local Environment Assessment; Namur)
- STAN server (STructure ANalysis - Ramachandran plots [More information] and "CA-Ramachandran" [More information] plots for proteins; Duarte-Pyle plots for nucleic acids; also runs the programs WASP and CISPEP; Uppsala)
- Ramachandran server (Bangalore)
- pdb-care (PDB CArbohydrate REsidue check; Heidelberg)
- Glossary (Maine)
Other biomolecules
- Nucleic Acid Database (Rutgers)
- RNABase (RNA structures; Johns Hopkins)
- SCOR, Structural Classification of RNA (Berkeley)
- GlycoSuiteDB (glycoprotein glycan structures; Sydney)
- pdb2linucs (carbohydrates in the PDB; Heidelberg)
- LIPIDAT (lipids; Ohio)
Small molecules
- ReLiBase (REceptor-LIgand interaction dataBASE; CCDC)
- LigBase (Database of Aligned Ligand Binding Sites; Rockefeller)
- ChemPDB (EBI)
- HIC-Up (Hetero-compound Information Centre - Uppsala)
- Hetero Components Database (Jena)
- PDL, Protein Ligand Database (Cambridge)
- Klotho (Biochemical Compounds Declarative Database; St. Louis)
- MathMol (Library of 3-D Molecular Structures; New York)
- HetSEL (Hetero-compound Search-Engine Launcher; Uppsala)
- CSD (CCDC Cambridge)
- More links
Specialised and derived structural databases and servers
- Structural databases in Nucleic Acids Research list (not all are specialised)
- PDBsum (EBI; new site !)
- PDBsum (UCL; old site !)
- SAS (Sequences Annotated by Structure; UCL)
- LPFC (core-structure database; Stanford)
- 3Dee (database of protein-domain definitions; Dundee)
- CDD (conserved domain alignments; NCBI)
- MolMovDB (Database of Macromolecular Movements; Yale)
- ElNemo (normal mode analysis; France)
- Dynamite (predict protein motions; Oxford)
- OLDERADO (NMR ensembles; Manchester)
- Representative NMR structure (MSD/EBI)
- PROMISE (mirror of discontinued site in Leeds; Scripps)
- COMe (bioinorganic motif database; EBI)
- Protein side-chain interactions (UCL)
- Side-chain and main-chain hydrogen bonding (UCL)
- SPIN-PP (Protein-protein interfaces; Columbia)
- PQS (quaternary structures of PDB entries; EBI)
- Quick PQS (quaternary structures of PDB entries; EBI)
- MutaProt (structural effects of point-mutations; Weizmann)
- ASTRAL (compendium for sequence and structure analysis; Berkeley)
- SLoop (database of super secondary fragments; Cambridge)
- Protein-Protein Interaction Server
- CADB, Conformation Angles DataBase (Bangalore)
- DSDBASE (disulfides; India)
- PMD, Protein Mutant Database (mutations mapped to structures; Japan)
Databases for specific protein families etc.
- Protein databases in Nucleic Acids Research list (not all have a structural component)
- Lectines (France)
- EyeSite (proteins in the eye; Birkbeck)
- Knottin (CNRS, France)
- Enzyme Structures Database (UCL)
- BRENDA (Comprehensive Enzyme Information System; Cologne)
- Histone Database (NIH)
- Homeodomain Resource (NIH)
- MEROPS (proteolytic enzymes; Sanger)
- AraC-XylS Database (CSIC)
- PKR (Protein Kinase Resource; SDSC)
- Antibodies - Structure and Sequence (Reading)
- SACS, Summary of Antibody Crystal Structures (Reading)
- MDB (Metalloproteins; Scripps)
- HIVdb (HIV proteases, up-to-date version; NIST)
- Prolysis (Proteases and protease inhibitors; Tours)
- CAZy (Carbohydrate Active Enzymes; CNRS)
- TIM-DB (TIM-barrel domains; Tarragona)
- Lipocalin Web Site (Jenner)
- ESTHER (alpha/beta hydrolases homologous to cholinesterases; INRA)
- NucleaRDB (database of nuclear receptors; UCSF)
- GPCRDB (G-protein coupled receptors; CMBI)
- EF-hand calcium-binding proteins data library (Vanderbilt)
- Serine Proteases (St Louis)
- SDAP, Structural Database of Allergenic Proteins (Texas)
- MemPro (Membrane-protein resources; Irvine)
Sequence databases and analysis and comparison servers
- SWISS-PROT (ExPASy)
- PIR
- NCBI
- GenBank
- EBI
- ExPASy
- EMBL
- Entrez (NCBI)
- ProSAL (Protein Sequence-Analysis Launcher; Uppsala)
- M.I.A., Molecular Information Agent (SDSC)
- META PP (Columbia)
- META PP (EMBL)
- BCM Search Launcher
- InterPro - Integrated Resource of Protein Families, Domains and Sites (EBI)
- PROSITE (ExPASy)
- BLAST (NCBI)
- ProDom (Toulouse)
- IBM (many servers of their Bioinformatics and Pattern Discovery group)
- PDBSprotEC (correspondence between DPB, SWISS-PROT and EC; Reading)
Multiple-sequence alignment
- Tcoffee@igs (Marseille)
- ClustalW, CAP, MAP, PIMA, MSA, Block Maker, MEME, Match-Box (BCM)
- ClustalW (EBI)
- ClustalW (EMBL)
- CLUSTALW (NPS@)
- POA (UCLA)
- MAFFT (Arkansas) Now also here and here in Kyoto.
- Match-Box (Belgium)
- Block Maker (FHCRC)
- MULTALIN (NPS@)
- MultAlin (Toulouse)
- Indonesia (free, Java-based program for multiple structure and sequence alignment, analysis and editing, pattern discovery, hidden Markov modelling, etc.; Uppsala)
- PRALINE (Amsterdam)
Literature
- Find "to be published" references in PDB entries (EBI)
- PubMed/Entrez (NCBI)
- WebMedLit (medical journals)
- BioMed Central (free, on-line papers)
- PubMed Central (free papers; NIH)
- HighWire (free papers; Stanford)
- PubMed Express (NIH)
- Infotrieve Article Finder
- Scirus scientific information
- ISI Web of Knowledge (Citation index)
- Libris (in Swedish)
- Electronic access to journals (only in Uppsala)
- BioMedNet (now deceased)
- PubCrawler
- Bioinformatics (journal)
- Genome Informatics (journal, papers are in English !)
- Ergito (web-based textbooks)
Structure prediction & modelling
- FoldIndex (predicts if a sequence will fold or not; Weizmann)
- DisEMBL (predicts if a sequence will be disordered or not; EMBL)
- GlobPlot (predicts order and globularity; EMBL)
- Protein Structure Prediction Center (home of CASP; LLNL)
- ModBase (Database of Comparative Protein Structure Models; Rockefeller)
- Gene3D (structural predictions for genes in whole genomes; UCL)
- Parts List (Yale)
- SUPERFAMILY (HMM-based predictions; Cambridge)
- FAMSBASE (homology models; Japan)
- 3D-Crunch (homology models; Geneva)
- GTOP, Genomes TO Protein structures and functions (Japan)
- PSSH, Protein Sequence-to-Structure Homologies (EBI)
- HSSP, Homology-derived Secondary Structure Prediction of proteins (EBI)
- List of structure prediction servers (Poland)
- Structure Prediction Meta-Server (Poland)
- BioServer (France)
- PredictProtein (predicts structural aspects based on a sequence; Columbia)
- Jpred2 (consensus secondary structure prediction; EBI)
- TMHMM (transmembrane helices and topology; Copenhagen)
- FOLD (fold recognition; UCLA)
- SAM-T99 (threading; UCSC)
- 3D-PSSM (threading; ICRF)
- 123D+ (threading; NCI)
- SWISS-MODEL (automatic homology modelling; Expasy)
- CPHmodels (automatic homology modelling; Copenhagen)
- Homology modelling for beginners (CMBI)
- Paper by Burkhard Rost (EMBL)
- Computational Chemistry Exhibition (Utrecht)
- FOLD-X (calculate folding pathway or stability of mutant structures; EMBL)
- Decoys 'R' Us (protein-like, but unreal structures; Stanford)
- ArchPRED (loop prediction server; AECoM)
Structural Genomics
- Overview (PDB)
- TargetDB (PDB)
- NIH Structural Genomics Initiatives
- PRESAGE
- PICASSO
- Crystallography 101 (LLNL)
- PSF (Protein Structure Factory; Berlin)
- NYSGRC (BNL)
- Yeast Structural genomics (France)
Crystallography
- EDS (Electron Density Server; Uppsala)
- TB Consortium Bias Removal Server (Texas A&M University)
- Crystal Twinning server (UCLA)
- Matthews Probability Calculator (LLNL)
- BCR (Biological Crystallization Resource; Canada)
NMR spectroscopy
- AQUA server (BMRB)
- AQUA server (Utrecht)
Various organisations, institutes etc.
- EMBO
- EMBL Heidelberg
- EBI Cambridge
- Linnaeus Centre for Bioinformatics (Uppsala)
- Stockholm Bioinformatics Centre
- Columbia University Bioinformatics Center (Uppsala)
- SBNet (Swedish Structural Biology Network)
- International Society for Computational Biology (ISCB)
- GenomeWeb.com (genomics news service)
- Bioinform (bioinformatics news service)
- Free patents site
- US Patent and Trademark Office
- CMBI (Nijmegen)
- UMBER (Manchester)
- EMBNet Sweden (Uppsala)
- CBS (Copenhagen)
- FEBS
- BioSci
- UK CropNet
- International Society for Computational Biology
Education
- 2can bioinformatics educational resource (EBI)
- Bioinformatics: a tutorial for beginners exploring human visual pigments (University of Southern Maine)
Various servers, resources etc.
- Nucleic Acids Research Database List
- Nucleic Acids Research database special 2004 (free access)
- Nucleic Acids Research Database List 2001
- Nucleic Acids Research web-servers special 2004 (free access)
- Nucleic Acids Research web-servers special 2003 (free access)
- DBCat (Catalog of Databases)
- Databases used by M.I.A.
- On-line Analysis Tools
- Computational Services at EMBL
- Tools at EBI
- Tools at ExPASy
- Scirus (scientific information searches)
- Google (search engine)
- WHAT IF servers (homology modelling, validation, graphics, analysis, etc.; CMBI)
- Pedro's BioMolecular Research Tools (Iowa)
- Pedro's BioMolecular Research Tools (Düsseldorf)
- Structure-related resources (York)
- CUBIC links
- BioSEL (Bio Search-Engine Launcher; Uppsala)
- KEGG (Kyoto Encyclopedia of Genes and Genomes)
- Protein Structure web site (accompanying Brändén and Tooze's book)
- Protein-Protein Interaction Server (UCL)
- Some biomolecular morphs and movies
- Amino acid repository (Jena)
- RESID, Post-translational modifications (PIR)
- Proteome analysis (EBI)
- DIP (Database of Interacting Proteins; UCLA)
- GETAREA (Solvent-accessible surfaces etc.; Texas)
- USF (Uppsala Software Factory)
- Cutter (proteolysis)
- PROWL (Mass spectrometry)
- Protein Prospector (Mass spectrometry)
- HGVBase (Human Genome Variation database)
- GeneLynx
- OMIM
- Molecule of the Month (PDB)
- Bioinformatics Resources
- Life-science dictionary
- The Biology Project
- CASTp (Pockets and cavities)
- PoPMuSiC (rational design of point mutations; Brussels)
- ConSurf (conservation mapped onto structure; Tel Aviv)
- PHT (metabolic pathway analysis; Cologne)
- NBCR (National Biomedical Computation Resource; San Diego)
- PCDDB (Protein Circular Dichroism DataBank; Birkbeck)
- GLYCOSCIENCES.de (databases and bioinformatics tools for glycobiology and glycomics; Heidelberg)
- Dombo Journal (if you need a break :-)

Practical "Structural Databases" - EMBO Bioinformatics Course - Uppsala 1999/2001 - Gerard Kleywegt