Center for Bioinformatics & Computational Biology

The RESID Database contains supplemental information on post-translational modifications for the standardized annotations appearing in the PIR-International Protein Sequence Database. The RESID Database includes: systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, indicators for N-terminal, C-terminal or peptide chain cross-link modifications, keywords, literature citations with database cross-references, structural diagrams and molecular models. Since 1995 updates of the RESID Database have appeared as often as weekly, and full releases appear quarterly. The database is freely accessible through the PIR Web site http://pir.georgetown.edu/pirwww/dbinfo/resid.html and by FTP.

The RESID Database is a comprehensive collection of annotations and structures for protein pre-, co-and post-translational modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link modifications. The RESID Database includes: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. This database is freely accessible on the Internet through the European Bioinformatics Institute at http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+ LibInfo+-lib+RESID, through the National Cancer Institute -Frederick Advanced Biomedical Computing Center at http://www.ncifcrf.gov/RESID, or through the Protein Information Resource at

The theme of the third annual Spring workshop of the HUPO-PSI was "proteomics and beyond" and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many of the HUPO-PSI XML interchange formats, minimal reporting requirements and accompanying controlled vocabularies were reported, with many of these now feeding into the broader efforts of the Functional Genomics Experiment (FuGE) data model and Functional Genomics Ontology (FuGO) ontologies.

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications and cross-links including pre-, co-, and post-translational modifications. The database provides: systematic and alternate names, atomic formulas and masses, enzymatic activities that generate the modifications, keywords, literature citations, Gene Ontology (GO) cross-references, protein sequence database feature table annotations, structure diagrams, and molecular models. This database is freely accessible on the Internet through resources provided by the European Bioinformatics Institute (http:// www.ebi.ac.uk/RESID), and by the National Cancer Institute -Frederick Advanced Biomedical Computing Center (http://www.ncifcrf.gov/RESID). Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries. As an Internet resource, the RESID Database assists researchers in high-throughput proteomics to search monoisotopic masses and mass differences and identify known and predicted protein modifications.

High-throughput proteomic studies produce a wealth of new information regarding post-translational modifications (PTMs). The Swiss-Prot knowledge base is faced with the challenge of including this information in a consistent and structured way, in order to facilitate easy retrieval and promote understanding by biologist expert users as well as computer programs. We are therefore standardizing the annotation of PTM features represented in Swiss-Prot. Indeed, a controlled vocabulary has been associated with every described PTM. In this paper, we present the major update of the feature annotation, and, by showing a few examples, explain how the annotation is implemented and what it means. Mod-Prot, a future companion database of Swiss-Prot, devoted to the biological aspects of PTMs (i.e., general description of the process, identity of the modification enzyme(s), taxonomic range, mass modification) is briefly described. Finally we encourage once again the scientific community (i.e., both individual researchers and database maintainers) to interact with us, so that we can continuously enhance the quality and swiftness of our services.

The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, highquality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.

UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/.

Pigheartmitochondrial malatedehy- drogenase (EC1.1.1.37), whichhasbeenobtained freeof electrophoretic subforms, has beenshown to havea molecular weightof67,000 andtobecomposedoftwopoly- peptide chains. Comparison oftheseandotherproperties, suchasamino-acid composition, isoelectric point,and keto-substrate inhibition, withthoseofL-3-hydroxyaeyl CoA dehydrogenase (EC1.1.1.35), anotherNAD+-depen- dentdehydrogenase ofmitochondrial origin, suggests structural similarities ofthetypeassociated withpro- teinspossessing common evolutionary origins. Thiscon- clusion issupported by immunological crossreactivity. In viewoftheseobservations, thedissimilarity inthe stereospecificity ofhydrogentransfer fromcofactor to substrate catalyzed bythetwoenzymesisattributed to 1800 rotation -inthebinding orientation ofthenicotinam- idemoietyoftheNAD+,ratherthantogrossdifferences inthegeometryoftheactive siteofthetwoenzymes. Comparisons ofthestructure-functi on relationships ofnumer- ousproteins haveprovide...