The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

By Nita Deshpande, K. J. Addess, Wolfgang Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie-Wen Xie, Li Chen, Zukang Feng and 5 more. Nucleic Acids Res., 2004

346 citations recorded by the source corpus.

The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules. The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data. The re-engineered site is currently in public beta test at http://pdbbeta.rcsb.org. The new site expands the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools. A new key feature is the integration and searchability of data from over 20 other sources covering genomic, proteomic and disease relationships. The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e76b8b2fc244687a0df2d2ec4d2141b701b600fe

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Structure-based Systems Biology for Analyzing Off-target Binding (2011, background): “Fortunately, in parallel with sequence growth, the structures deposited in the Protein Data Bank [21] have also been increasing at a very fast rate.”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, background): “The number of experimentally determined structures deposited in the Protein Data Bank (PDB) more than doubled from 23 096 to 52 821 over the last 5 years (September 2008) (4).”
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures (2007, background): “The database of atomic-resolution RNA 3D structures is growing rapidly [6,7,11,21] and now includes ribozymes [1,14,25], ribosomal subunits [3,16,44] and intact 70S ribosomes [42].”
Machine learning approaches and databases for prediction of drug–target interaction: a survey paper (2020, methodology): “The data stored in PDB-bind were classified by the biomolecular complex data from PDB.”
ModBase, a database of annotated comparative protein structure models and associated resources (2013, background): “The number of experimentally determined structures deposited in the Protein Data Bank (PDB) more than doubled from 23 096 to 52 821 over the last 5 years (September 2008) ( 4 ).”
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns (2007, background): “However, the number of experimental phosphorylation sites located in the protein regions with known structure from PDB (22) is few for each kinase-specific group.”
The UCSC Genome Browser Database: update 2006 (2005, background): “Known or predicted 3D structures from PDB (17) or ModBase (18) are displayed, with links to those sites for more information.”
MODOMICS: a database of RNA modification pathways—2013 update (2012, methodology): “Accession numbers from the Swiss-Prot (39) and GenPept (40) databases are provided and proteins with experimentally determined structures are linked to appropriate entries in the Protein Data Bank (41).”
Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis (2009, methodology): “215 non-redundant proteins with NAD co-factors were downloaded from the RCSB Protein Data Bank (PDB) [40,43].”
MODOMICS: a database of RNA modification pathways. 2008 update (2008, background): “The chemical structures of modiﬁed nucleosides are represented by 1D SMILE codes, 2D structure plots and 3D structures in the Protein Data Bank format displayed interactively on the website by a Jmol applet.”
The Universal Protein Resource (UniProt): an expanding universe of protein information (2005, background): “InterPro (12), Pfam (13)], protein structure [e.g. PDB ( 14 )], ontology [e.g.”
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education (2014, methodology): “PDB data are loaded into the RCSB PDB relational database (20,21) and enhanced by integrating them with other biological data sources (2,22) and computed information (23) to provide a ‘Structural View of Biology’ on the RCSB PDB website.”
The RCSB Protein Data Bank: redesigned web site and web services (2010, background): “Here, we describe major new or expanded features from those reported 5 years ago (5), including new query and”
Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “In this example, six PDB sequences show very signiﬁcant similarities to the query sequence, with E -values equal to 0.”
SuperTarget and Matador: resources for exploring drug-target relationships (2007, background): “In a last step, relations from other databases, namely DrugBank (3), KEGG (9), PDB (10), SuperLigands (11) and TTD (4), were checked for drug-target interactions not identified with the preceding steps.”
CEP: a conformational epitope prediction server (2005, methodology): “Predictions for 1800 proteins with resolution better than 1.5 s (PDB release dated April 5, 2005) are available on the server and can be browsed using PDB ID.”