The RCSB PDB information portal for structural genomics

By Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman. Nucleic Acids Res., 2005

459 citations recorded by the source corpus.

The RCSB Protein Data Bank (PDB) offers online tools, summary reports and target information related to the worldwide structural genomics initiatives from its portal at . There are currently three components to this site: Structural Genomics Initiatives contains information and links on each structural genomics site, including progress reports, target lists, target status, targets in the PDB and level of sequence redundancy; Targets provides combined target information, protocols and other data associated with protein structure determination; and Structures offers an assessment of the progress of structural genomics based on the functional coverage of the human genome by PDB structures, structural genomics targets and homology models. Functional coverage can be examined according to enzyme classification, gene ontology (biological process, cell component and molecular function) and disease.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8da7a7989be522aa30bd31f218a97e49c5dfe36c

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Citations in the corpus

Database resources of the National Center for Biotechnology Information (2006, methodology): “The NCBI MMDB, built by processing entries from the Protein Data Bank (5), is described in (33).”
The case for cloud computing in genome informatics (2010, background): “For instance, they could accept external disks shipped by mail the way that the Protein Database [52] once accepted atomic structure submissions on tape and floppy disk.”
PDBe: Protein Data Bank in Europe (2010, methodology): “SIFTS data is used by major bioinformatics resources such as RCSB (5), PDBsum (31), Pfam (17), SCOP (27), InterPro (29), several DAS server providers (32) and many research and service groups around the world to provide cross-reference information on their web pages.”
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis (2013, methodology): “NIP pairs were derived from 3D structures of PDB biological units (24) as described in the original Negatome 1.”
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes (2009, background): “Links to other major databases such as UniProt (5), PDB (6) and Pfam (7) are also maintained.”
A position-specific distance-dependent statistical potential for protein structure and functional study (2012, methodology): “The simple counting method does not work for our potential simply because there is not enough number of solved protein structures in the PDB for reliable counting of sequence profile contexts.”
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee (2006, background): “The increasing availability of structural data (5) means that relying on structure-based methods for sequence analysis has become much more realistic than it used to be.”
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource (2012, methodology): “Finally, the SIFTS data are made available through DAS servers at RCSB (http://www. pdb.org/pdb/rest/das/ based on http://biojava.org/wiki/ Dazzle) and EBI (http://www.ebi.ac.uk/das-srv/pro teindas/das/pdbe_summary).”
Database resources of the National Center for Biotechnology Information: update (2004, methodology): “The NCBI MMDB, built by processing entries from the Protein Data Bank ( 5 ), is described in (33).”
Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments (2008, methodology): “In the second test the fragment classes were used to reconstruct the backbones of all known human structures in the Protein Data Bank (PDB) using a novel backbone coverage algorithm.”
Statistical potential for assessment and prediction of protein structures (2006, background): “For example, neither was arbitrarily chosen to correspond to the first separately listed structures in the 2pna PDB file.”
DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs (2010, background): “For instance, version 2.0 of DrugBank contained up to 18 database hyperlinks in every DrugCard entry, including links to KEGG (9), PubChem (7), ChEBI (10), PharmGKB (6), PDB (18), GenBank (19), DIN, RxList, PDRhealth, Wikipedia, ATC, UniProt (16), Pfam (20), dbSNP (17), GeneCards (21), GenAtlas (22)”