Protein/Amino Acid Databases

	FRONTIERS IN BIOSCIENCE; DATABASES; PROTEIN/AMINO ACID
	Due to the large number and variation in content of the databases, we have tried to arrange the links available into some sort of system to allow an investigator to quickly find an appropriate database without having to read through a mass of links. Much of the system works by using internal hypertext indexing within the page. Note that hypertext links with square brackets, `[ ]', are internal indexing links to another part of this page. Database sites are listed primarily according to whether they fall into the following catagories. [ Classificational ] [ Complex ] [ Correlational ] [ List ] [ Specific ] [ Updates ] COMPLEX DATABASES Extensive informational content on protein images, structure, sequences, homologies, classification, physical properties etc Molecules R US: - Interactive text and images of [ PDB ] files at NIH [ NIH ] NRL_3D: - Sequence/structure database at [ JHU ] NRL_3D: at EMBL [ Heidelberg ] OWL: - Non-Redundant Protein Sequence Database at John Hopkins [ JHU ] [ OWL: ] - UCL Mirror in London [ UCL ] Protein DataBase: - PDB information and service listings at Brookhaven National Laboratory [ BNL ] PDB-Browser: at [ BNL] [ PDB: ] - GenomeNet Mirror, in [ Japan ] [ PDB: ] - U. Genova Mirror [ PDB: ] - PDB-List: and PDB-Annotated: at Brussels Free U. [ PDB: ] - PDB-Select: at [ EMBL ] (See below) Biological Units: - Expanded [ PDB ] entries with full biological units at [ BNL ] PDBSTR: - Reorganized Protein Data Base ([ PDB ]) to standardize file types at GenomeNet, [ Japan ] PIR: - Protein Identification Resource database at [ JHU ] PRF: - Protein Research Foundation database at GenomeNet SwissProt - Protein database at ExPASy [ Switzerland ] SPECIFIC DATABASES Informational content restricted to specific subjects or file types with additional information via external links BioMagResBank: - Database of NMR-derived protein structures at BIMAS-NIH Kabat: - Database of proteins of immunological interest at [ JHU ] Kinemage-Index: - "Kinetical Images" by protein type at Protein Science MPDB: - Molecular Probe Data Base at [ EMBL ] [ MPDB: ] Gopher in U. Agricultural Sciences, Sweden Swiss-2DPage: - Two-dimensional protein polyacrylamide gel electrophoresis database at [ ExPASy ] TFFACTOR: and TFSITE: - Transcription Factor Data at [ EMBL ] TREMBL: - Database of translated peptide sequences of all CDS features from EMBL sequences at [ EMBL ] CORRELATIONAL DATABASES Databases which hold information on correlations between protein: [ Sequence ] [ Structure ] [ Homolgy ] [ Domain ] [ Combination ] PIRALN: - Database of sequence alignments based on [ PIR ] at [ EMBL ] PRINTS: - Protein motif fingerprints database (see Documentation) PRINTS-ALIGN: at [ UCL ] PRINTS: at EMBnet-Basel, Switzerland PROSITE: - Protein sites and patterns database at ExPASy PrositeScan: at ISREC, Switzerland PROSITE-Search: at [ EMBL ] DSSP: - Database of secondary structure of proteins from [ PDB ] (see Documentation) at [ EMBL ] FSSP: - Database of families of structurally similar proteins in [ PDB ] at [ EMBL ] BLOCKS: - Database of homology regions in proteins and BLOCKS-WAIS: at Fred Hutchinson Cancer Research Center BLOCKS: at [ EMBL ] and BLOCKS-Search: from Iowa State HSSP: - Database of homology-derived structures of proteins based on [ PDB ] and [ EMBL ] ProDom: - A Protein Domain database and ProDom-Search: at INRA-Toulouse ProDom: and ProDom-Search: at Sanger Centre, UK ProDom: at [ EMBL ] PUU: - Protein domains database based on [ EMBL ] SWISSDOM: - [ SwissProt ] entries as a [ ProDom ] Map at EBI, UK AllAll: - Database of a set of related peptides at ETH-Zürich, Switzerland PDBFINDER: - Database of [ PDB ], [ DSSP ] and [ HSSP ] Information (see Documentation)at [ EMBL ] ProLink: - Integrated database of protein structure, homology, and functional pattern at BMERC 3D-ALI: - Database relating Proteins Structures and Sequences (see Documentation) at [ EMBL ] CLASSIFICATIONAL DATABASES Databases structured for protein classification information CATH: - Class, Architecture, Topology and Homology hierarchical protein structure classification at [ UCL ] EC Enzyme: at [ JHU ] EC Number Table: at GenomeNet ENZYME: - The Enzyme nomenclature database at [ ExPASy ] Enzyme Structures Database: - Structures of enzymes in the [ PDB ] at [ UCL ] GenoBase Enzyme Index: at [ NIH ] PDB At A Glance: - Access to [ PDB ] files by classification hierarchy at [ NIH ] SCOP: - Structural Classification Of Proteins at Cambridge, UK DATABASE UPDATES Sites containing database update information Protein-Extras: at [ EMBL ] PDB-Index: at [ BNL ] PDB-Pending: at [ BNL ] SWISSNEW: - New [ SwissProt ] sequences at EBI LIST OF PROTEIN DATABASES AA-Index (Amino Acid Index Database) Search box entry. 402 entries. Amino AcidsGerman and English. Chemical formula, and structure, Alchemy MIME type 3D models. AA Properties Formula, structure, masses, physical and chemical properties, references. AA Notations and Properties Single file of two ascii graphic tables. AA Images with Atomic Numbering All-in-one image or one image per amino acid. AA/Protein Side-Chain Interactions How amino acid side chains pack against one another AA Side-Chain and Main-Chain Hydrogen Bonding Hydogen bonding of amino acid side chains CATH (Protein Structure Classification) FSSP (Database of Families of Structurally Similar Proteins derived from PDB) GenQuest (Search against a protein database with the Q server) HHS (SwissProt and PDB Systematic Sequence Classification Database) HSSP(Database of Homology-Derived Structures of Proteins based on PDB and SwissProt) Kabat (Database of Proteins of Immunological Interest) List of Protein Nomenclature References (References on Protein Nomenclature and Terminology) LITDB (PRF Protein/Peptide Literature Database) MassSearch (Search SwissProt or EMBL Databases by Protein Mass After Digestion) MHCPEP (Database of Major Histocompatibility Complex [MHC] Binding Peptides) NRL_3D (Sequence/Structure Database derived from PDB) NuclPepSearch (Search SwissProt for a Nucletide Sequence) NYC-MASS (Protein Mass Spectrometry Database) OWL (Non-Redundant Protein Sequence Database [Updated Daily]) OWLREF (Search the References of OWL; Non-Redundant Protein Database) Protein database (PDB) PDB-List (Brussels) PDB-Annotated (Brussels) PDB (GeneomeNet, Japan) PDB (Italy) PDB At A Glance (Hierarchic Access to PDB Files) PDB Browser PDBFINDER (A Database Containing PDB, DSSP and HSSP Information) PDB Gopher PDB Index PDB Pending PDB Select (EMBL-Heidelberg) PDBSTR (Re-organized Protein Data Bank) PDD (Protein Database; Disease) PIR (Protein Identification Resource Database) PMD (Protein Mutant Database; EMBL-Heidelberg) PMD (Protein Mutant Database;Japan) PMOTIF (Search Protein Motifs in Gene Sequence) PRF (Protein Research Foundation Sequence Database) PRINTS (Protein Motif Fingerprints Database) Protein Families (Links to Information on Different Protein Families) Protein Motions (DataBase of Protein Movements) PUU (Protein Domains Database Based on PDB-Select) SBASE (Library of Protein Domains) SCOP (Structural Classification of Proteins) Sleuth (Amino Acid Conformation and Solvent Accessibility of PDB Files) SWISSNEW (New SwissProt Sequences) SwissProt (Protein Sequence Database) Swiss-Shop (Automated SwissProt and Prosite Information Queries)