Databases

Miscellaneous

• Hypertext Entrez
  • How to search Entrez
  • About the WWW Entrez Databases
  • Find MEDLINE articles that match a given text

• ENZYME Database at ExPASy: A repository of information relative to the nomenclature of enzymes as established by the Nomenclature Committee of IUBMB.
• John Hopkins University: An Enzyme Classification Database.
• SWISS-2D PAGE at ExPASy: 2D electrophoresis database.
• 2D PAGE Databases (Human and Mouse) at Danish Centre for Human Genome Research
• O-GLYCBASE at the Center for Biological Sequence Analysis: Database of O-glycosylated proteins (over 100 proteins and 600 O-glycosylation sites)

• Hypertext SwissProt (European Protein Database)
• Hypertext Prosite (European Protein Sequence Motifs Database)
  Search the European Databases (EMBL, Swissprot etc) with a complex search or by accession number
• Stanford Genome Project: contains yeast and C. elegans comparison
• TIGR Database: The Institute for Genomic Research This site contains links to numerous data bases in bacteria, plants, and animals (including humans).

• PDB (Protein Data Bank) A database of experimentally determined three-dimensional structures of biological macromolecules.
• Atlas of Protein Side-Chain Interactions
• Protein Database Structural Medicine Links, Includes many protein structure databases and search tools to complete exhaustive 3D structure comparison of protein structures currently in the PDB.

• BLITZ Database Searches
• Prodom search
• Search Prosite (for protein signature sequences)

Protein Motifs and Domain

• PROSITE at ExPASy: Database of biologically significant sites, patterns and profiles in proteins.
• PRINTS Database: Protein motifs fingerprint database (fingerprint= group of conserved motifs used to characterize a protein)
• Pfam: Protein FAMilies Database at Sanger Center: High-quality comprehensive collection of protein domain families.

• Brutlag Bioinformatics Group: Bioinformatics applications developed by this Stanford Biochemistry Research Group are available at this site. It includes ALION (aligns sequences), EMOTIF (forms motifs for subsets of aligned sequences), Identify (a system for identifying the proteins to which a sequence belongs), Lock (align a protein sequence to a target sequence) and SCAN (search protein databases for proteins containing a particular motif). Numerous links relating to bioinformatics.
• GenomeNet: Data base retrieval, KEGG (Kyoto Encyclopedia of Genes and Genomes), Sequence interpretation tools, and genome data bases in Japan
• Guide to sequence analysis at Harvard
• NCBI Molecular Biology Tools
• Pedro's BioMolecular Research Tools: This site contains multiple a collection of WWW links to information and services useful to molecular biologists.
• Swiss-Model (Automated Protein Homology Modelling)

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