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ALIGN ALIGN is a compendium of protein sequence alignments: it is a companion resource to PRINTS. For each fingerprint, there is a corresponding alignment in NBRF format, the root name of which is the relevant PRINTS code.
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 (current version), retrieve blocks, and create new blocks, respectively. The blocks for the Blocks Database are made automatically by looking for the most highly conserved regions in groups of proteins documented in the Prosite Database.
CODONTREE  A database that is able to determine the codon usage table for a set of protein coding genes; gene relationships on the basis of codon usage similarity; and compositional features of protein coding genes.
COGs: Clusters of Orthologous Groups of Proteins COGs were delineated by comparing protein sequences encoded in 21 complete genomes, representing 17 major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
DIP: Database for Interacting Proteins This set of Web pages will allow you to: search the DIP database, to submit new protein-protein, and to update database entries by adding new references to the DIP.
EBI_Swiss-PROT An annotated protein sequence database established in 1986 and maintained collaboratively by the Swiss Institute of Bioinformatics (SIB) and the European Bioinformatics Institute (EBI).
ECOWEB: ECOGENE WEB SITE A collection of information about the genes, proteins, and intergenic regions of the E. coli K-12 genome and proteome accumulated during years of sequence analysis and literature surveys.
ExPASy_ENZYME A repository of information relative to the nomenclature of enzymes.
ExPASy_PROSITE A database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs.
ExPASy_SWISS-PROT Sequence retrieval from SWISS-PROT and TrEMBL.
ExPASy_SWISS-2DPAGE A two-dimensional polyacrylamide gel electrophoresis database. It contains data on proteins identified on various 2-D PAGE reference maps. SWISS-2DPAGE contains data on proteins identified on various 2-D PAGE reference maps.
ExPASy_TrEMBL A protein sequence database supplementing the SWISS-PROT Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in SWISS-PROT.
ExPASy_TrEMBL_NEW Consists of the translation of all new and updated CDS in EMBL since the last TrEMBL release. It is partially redundant with SWISS-PROT and TrEMBL.
Genprotec: E.coli Genome and Proteome Database A database dedicated to E. coli genome and proteome. It aims to provide biochemists with the most updated and consolidated information about E. coli genes and proteins resulted from both the traditional experimental research and our computational analysis.
Histone Sequence Database This database is a compilation of entries from SWISS-PROT, PIR, PDB, and CDS translations from GenBank.
Kabat Database of Sequences of Proteins of Immunological Interest The Kabat Database of Sequences of Proteins of Immunological Interest.
ModBase: Database of Comparative Protein Structure Models A queryable database of annotated protein structure models. The models are derived by ModPipe, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database also includes fold assignments and alignments on which the models were based. MODBASE contains theoretically calculated models, which may contain significant errors, not experimentally determined structures.
MOTIF For searching protein and nucleic acid sequence motifs.
NCBI_GenBank An annotated collection of all publicly available nucleotide and amino acid sequences.
NCBI_RefSeq: Reference Sequence Project A database of non-redundant reference sequences standards, including genomic DNA contigs, mRNAs and proteins for known genes. These provide a stable reference point for mutation analysis, gene expression studies, and polymorphism discovery.
OWL: Composite Protein Sequence Database A non-redundant composite of 4 publicly-available primary sources: SWISS-PROT, PIR, GenBank (translation) and NRL-3D. SWISS-PROT is the highest priority source, all others being compared against it to eliminate identical and trivially-different sequences.
PepPepSearch Search Swiss-Prot for a peptide sequence.
Pfam: Protein Families Database of Alignments and hMMs A large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Pfam is a collection of protein families and domains. Pfam also contains multiple protein alignments and profile-HMMs of these families.
PhosphoBase A database of phosphorylation sites in proteins.
PMD: Protein Mutant Database PMD covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globulin and immunoglobulin families. The PMD is based on literature, not on proteins.
PRF/SEQDB: Protein Research Foundation PRF/SEQDB is the database of protein primary structures. SEQDB contains sequence-related information as well as protein primary structures reported in scientific journals.
PRINTS: Protein Fingerprint Database A compendium of protein fingerprints. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space.
ProDom A database and its server have been designed as a tool to help analyze domain arrangements of proteins and protein families. The ProDom protein domain database consists of an automatic compilation of homologous domains.
Protein Loop Classification This databank contains conformational clusters and consensus sequences for protein loops that have been derived by computational analysis of their structures in a non-redundant set of proteins with less than 25% sequence homology (X-ray resolution better than 2.5 A).
ProtoMap An automatic hierarchical classification of all SwissProt proteins. This site offers an exhaustive classification of all proteins in the SwissProt database, into clusters of related proteins. The resulting classification splits the protein space into well defined groups of proteins, most of them are closely correlated with natural biological families and superfamilies.
REBASE: The Restriction Enzyme Database A collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952). Updated daily.
RNA Helicases From Saccharomyces cerevisiae A list of all putative RNA helicases from the sequencing of the entire Saccharomyces cerevisiae genome.
SBDS Analyzes the amino acid composition of a protein.
SWISS-Prot Protein Sequence Database An annotated protein sequence database. The SWISS-PROT protein sequence database consists of sequence entries. Sequence entries are composed of different line types, each with their own format. Annotation, Minimal redundancy, Integration with other databases.
The Molecular Biology Database Collection of NAR (Nucleic Acids Research) The Nucleic Acids Research Molecular Biology Database Collection is a public online resource that lists the databases described in the issues of Nucleic Acids Research together with other databases of value to the biologist and available throughout the world. All databases included in this Collection are freely available to the public.
Telomere proteins Database A telomere proteins information center supported by NIH. Telomere literature references are accessible through a searchable Telomere Literature Database.
THE SANGER CENTRE_WORMPEP A Caenorhabditis elegans protein database. Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.
UniProt: The Universal Protein Information Resource A comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.

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