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Contents: Databases

  1. Databases, general
  2. Databases, miscellaneous
  3. Databases, nucleotide sequences
  4. Databases, protein sequence information
  5. Databases, protein structure information



Databases

Databases, general


Databases, miscellaneous
  • Malaria db:     Dep. of Microbiol., Monash Univ. and The Walter and Eliza Hall Inst. of Medical Research, Australia
  • Malaria (Parasitology):     Other Malaria and Parasitology Sites, Monash Univ., Australia
  • Parasite genome db:     Parasite genome databases and genome research resource, EBI, UK.
  • PDD:     Protein Diseaseb
  • GIF_DB:     Genes Interactions in the Fly DataBase, Marseille, France. A specialized database for Interactions involved in Pattern formation in Drosophila
  • TBASE:     TBASE
  • GPCRDB:     Information system for G protein-coupled receptors (GPCRs), EMBL, Heidelberg, Germa.
  • Cytokine dbCFC:     Cytokine Family cDNA Database (dbCFC), Kumamoto Univ., Japan
  • HLDA (Hum Leukocyte Diff Antig):     Human Leukocyte Differentiation Antigens (HLDA), resource page, Japan


Databases, nucleotide sequences
  • EMBL:     Nucleotide Sequence Database (EBI)
  • NCBI:     GenBank
  • NDB:     Nucleic Acid db (Ruttgers)
  • NCGR:     The Genome Sequence DataBase (NCGR)
  • Ensembl Project:     Ensembl project for automatic annotation of eukaryotic genomes.
  • Vector seq:     Vector sequence db (Queen's Univ, Canada)
  • Univ. Illinois:     The Ribosomal Database Project (Univ of Illinois, Urbana, USA)
  • Univ. Antwerb:     Large ribosomal subunit db (Univ Antwerpen, Belgium)
  • Univ. Antwerp:     Small ribosomal subunit db (Univ Antwerpen, Belgium)
  • Univ. Texas:     uRNA db (Univ of Texas, Tyler, USA)
  • Univ. Utah:     RNA modification db (University of Utah, Salt Lake City, USA)
  • IST,Genova:     The molecular probe db (IST, Genova, Italy)
  • Univ Nijmegen:     PCR primers db (Univ Nijmegen, Netherlands)
  • Kazusa:     Codon usage db (Kazusa DNA Research Institute, Japan)
  • CBS,Den:     DOGS (Database Of Genome Sizes, CBS, Denmark)


Databases, protein sequence information
  • SWISS-PROT:     database of protein sequens
  • PIR:     Sequence Database
  • PROSITE:     Dictionary of protein sites and patterns. PROSITE is a method of determining what is the function of uncharacterized proteins translated from genomic or cDNA sequences. It consists of a database of biologically significant sites, patterns and profiles that help to reliably identify to which known family of protein (if any) a new sequence belongs
  • BLOCKS:     Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Block Searcher, Get Blocks and Block Maker are aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks, retrieve blocks, and create new blocks, respectivel
  • PRINTS:     PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of OWL. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs: the database thus provides a useful adjunct to PROSITE
  • MOTIFS:     A set of motif libraries and search programs (Kyoto Univ., Japan) for retrieval and analysis of protein sequence and structural motifs. The program currently availables
  • CDD:     Conserved domain db and search service.
  • ProDom:     The ProDom protein domain database consists of an automatic compilation of homologous domains detected in the SWISS-PROT database by the DOMAINER algorithm (Sonnhammer, E.L.L. & Kahn, D., 1994, Protein Sci. 3:482-492). It has been devised to assist with the analysis of the domain arrangement of protein
  • PUU:     Putative protein structural domai.
  • Modules:     The module pages contain information and research tools on mobile protein domai.
  • ProtoMap:     Automatic hierarchical classification of all SWISSPROT and TrEMBL proteins.
  • Yeast db:     YPD contains physical, functional, and genetic information for the proteins of budding yeast, Saccharomyces cerevisi.
  • Kabat db:     The Kabat database of sequences of proteins of immunological intere.
  • REBASE:     EC-ENZYME database
  • BRENDA:     BRENDA-Comprehensive enzyme information system.
  • ENZYME:     enzyme nomenclature db
  • Univ College,London:     Enzyme Structures
  • TBASE:     The Transgenic/Targeted Mutationbase
  • PDD:     Protein Diseasebase
  • O-GlycBase:     O-GLYCBASE is a revised database of O-glycosylated proteins (CBS, Denmark).


Databases, protein structure information
  • PDB (Rutgers):     The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students.
  • PDB (Brookhaven):     The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students.
  • BMCD:     The biological macromolecule crystallization db and the NASA archive for protein crystal growth data.
  • BioMagResBank:     Protein, peptide and nucleic acid NMR spectroscopy db.
  • Klotho:     Biochemical compounds declarative db.
  • DSSP:     DSSP database of secondary structure assignments for proteins of known structure. Contains information about secondary structure, solvent accessibility and some contacts for all PDB proteins.
  • HSSP:     HSSP database of homology-derived secondary structure of proteins. It contains the alignments of all known structures against the SWISS-PROT sequence data base.
  • FSSP:     FSSP database of fold classification based on structure-structure alignment of proteins. Contains the structural all-against all alignments for PDB.
  • PDBFINDER:     The PDBFINDER database is a database that is constructed from the PDB, DSSP and HSSP databases. Many of the fields contained in the PDBFINDER database are difficult to access from the original databases. Some information is retrieved from the original literature.
  • Univ College,Lon:     Enzyme Structures db
  • SCOP:     Classification of protein structures into structural families and display of 3D structure.
  • CATH:     Classification of protein structures into structural families. CATH is based on both structural and sequence relationships between proteins at several levels of similarity.
  • ProDom:     The ProDom protein domain database consists of an automatic compilation of homologous domains detected in the SWISS-PROT database by the DOMAINER algorithm (Sonnhammer, E.L.L. & Kahn, D., 1994, Protein Sci. 3:482-492). It has been devised to assist with the analysis of the domain arrangement of proteins.
  • Protein Potential Site:     Resources for development and application of potential.
  • PUU:     Putative protein structural domains.
  • SWISS-3DIMAGE:     High quality pictores of biological macromolecules.
  • Protein Motions:     A db of domain, loop and subunit motions.


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