The Protein Data Bank: unifying the archive

By John D. Westbrook, Zukang Feng, Shri Jain, Talapady N. Bhat, Narmada Thanki, V. Ravichandran, Gary Gilliland, Wolfgang Bluhm, H. Weissig, D. S. Greer and 2 more. Nucleic Acids Res., 2002

312 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/41aa810fdc349f6778f520f4a11505f889bb1291

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Citations in the corpus

SCOP database in 2002: refinements accommodate structural genomics (2002, background): “These domains correspond to 12 794 entries in the Protein Data Bank (3,4) and 39 references from the literature, for which the experimental coordinates are not available.”
BIND: the Biomolecular Interaction Network Database (2003, methodology): “Recently, all molecular interactions in PDB (9) were imported into BIND, via the validated MMDB database (10), using MMDBBIND (11).”
SCOP database in 2004: refinements integrate structure and sequence family data (2004, background): “Twenty-seven of the 28 remaining proteins in SCOP 1.63 were found by a recent inspection to have closely related representative structures in PDB and were made obsolete.”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, background): “The number of experimentally determined structures deposited in the PDB increased from 23 096 to 31 823 over the last 2 years (August 2005) (4).”
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. (2003, methodology): “The statistical and comparative analyses are compiled using InterPro, CluSTr (Kriventseva et al. 2001), and GO and contain structural information derived from the HSSP (Dodge et al. 1998) and PDB (Westbrook et al. 2002) databases.”
LIGAND: database of chemical compounds and reactions in biological pathways (2002, methodology): “We have added several links to other databases such as OMIM (6) for human genetic diseases, PROSITE (7) for amino acid sequence motifs, PDB (8) for protein structures, in addition to PATHWAY and GENES databases in KEGG.”
Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. (2003, background): “Much effort is going into unifying and cleaning PDB data to improve it and to eliminate inconsistencies.(3,4) This rapid increase in data, accompanied by the correction of erroneous data will significantly extend the value of 3D protein structures for drug development.”
ModBase, a database of annotated comparative protein structure models and associated resources (2013, background): “The number of experimentally determined structures deposited in the PDB increased from 23 096 to 31 823 over the last 2 years (August 2005) ( 4 ).”
PISCES: a protein sequence culling server (2003, methodology): “The resolution and R-value data are also obtained from the Uniformity Project files, since the RCSB has gone to some effort to place these values in a standard format in these files.”
MIPS: analysis and annotation of proteins from whole genomes in 2005 (2005, background): “Additionally, secondary structures and trans-membrane segments are predicted using standard algorithms, and a 3D structure ( 17 ) is assigned to the sequence whenever possible.”
The Database of Interacting Proteins: 2004 update (2004, methodology): “In addition to the information extracted from the research literature, the database has been recently enriched with information obtained by analyzing the structures of protein complexes deposited in the Protein Data Bank (9).”
PISCES: recent improvements to a PDB sequence culling server (2005, methodology): “These mmCIF files are a result of the Uniformity Project, an effort by the RCSB to standardize and correct information across all the PDB files (15,16).”
Accomplishments and challenges in literature data mining for biology (2002, background): “NREF provides comprehensive protein sequence data with source attribution and minimal redundancy (Fig.”
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema (2004, methodology): “In order to improve the accessibility of the PDB’s structure data, display the increased level of detail and improved consistency resulting from the RCSB PDB data uniformity project ( 3 ,4), and take advantage of advances in database and Web/Internet technologies, the RCSB PDB has re-engineered its ”
Can correct protein models be identified? (2003, methodology): “We chose to use a data set from LiveBench-2 performance of different fold recognition Web servers by submitting the sequence of recently solved proteins structures with no obvious close homolog (10 −3 BLAST cutoff; Altschul et al. 1997) to a protein in the Protein Data Bank (Westbrook et al. 2002).”
AtomEye: an efficient atomistic configuration viewer (2003, background): “The Protein Data Bank (PDB) [12] atomic structure file format, though widespread with great impact, does have drawbacks such as fixed (and therefore possibly insufficient) digits/accuracy, no velocity specification standard (for molecular dynamics), and is uncompressed.”