Prot Reference Clusters (UniRef) speed similarity searches via sequence space compression by merg-ing sequences that are 100 % (UniRef100), 90% (UniRef90) or 50 % (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data

One of the critical issues in bioinformatics is the data structure used for representing the protein data; this representation is a base for the operations applied such as sequence alignment, structure alignment and motif finding. In this paper, a survey of different representations and wellknown

-uled for intense sequence analysis. The content of Entrez Gene represents the result of both curation and automated integration of data from NCBI’s Reference Sequence project (RefSeq), from collabo-rating model organism databases and from other databases within NCBI. Records in Entrez Gene are assigned unique

interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions

descriptions of constituent molecules in experimentally determined 3D macromolecules

the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching

Motivation: Integral membrane proteins play important roles in living cells. Although these proteins are estimated to constitute around 25 % of proteins at a genomic scale, the Protein Data Bank (PDB) contains only a few hundred membrane proteins due to the dif-ficulties with experimental

that underlie many biological phenomena, including protein folding and enzyme catalysis. The PPD serves as a general protein pKa archive and as a source of data that allows for the development and improvement of pKa prediction systems. The database is accessed through an HTML interface, which offers two fast

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and EM depositions to the PDB (Berman et al., 2000)