The Protein Data Bank and structural genomics

By John D. Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M. Berman. Nucleic Acids Res., 2003

404 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ecf106252d5c0246df11187a6ae49d4556ffb08d

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

GeneSilico protein structure prediction meta-server (2003, methodology): “A local PDB-BLAST filter for identification of closely related sequences of known structures in PDB [prediction is halted and the user is notified if E-value <10 3 is reported in the PSI-BLAST (8) search against the PDB database (19)].”
The Genomes of Oryza sativa: A History of Duplications (2005, background): “The known interactions are taken from numerous sources, including Protein Data Bank [42] and the Database of Interacting Proteins (which stores yeast two-hybrid studies, affinity column studies, and literature searches) [43].”
VADAR: a web server for quantitative evaluation of protein structure quality (2003, background): “Here we wish to describe a web server, called VADAR, that is able to accept PDB formatted coordinate files and calculate, graph, report and/or evaluate a large number (>30) of key structural parameters for the entire protein as well as numerous structure descriptors for individual atoms, side chains”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, background): “NCBI-nr [31,32] is the single largest publicly available protein resource and includes protein sequences submitted to SWISS-PROT (curated protein database) [122], PDB (a database of amino acid sequences with solved structures) [123], PIR (Protein Information Resource) [124], and PRF (Protein Researc”
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. (2005, methodology): “Structural context of O-glycosylation sites The Protein Data Bank (Westbrook et al., 2003) was scanned for structural information about the protein sequences in our data set.”
UniProt archive (2004, methodology): “New and updated protein sequences are loaded daily from public databases including SWISS-PROT, TrEMBL, PIR-PSD, EMBL (Stoesser et al., 2003), Ensembl (Hubbard et al., 2002), PDB (Westbrook et al., 2003), IPI (http://www.ebi.ac.uk/IPI), RefSeq (Pruitt and Maglott, 2001), FlyBase (The FlyBase Consorti”
SWISS-MODEL: an automated protein homology-modeling server (2003, methodology): “Currently, about 20 000 experimental protein structures are deposited in the Protein Data Bank (PDB) (1).”
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models (2004, background): “Model coordinates can be downloaded in PDB format or as DeepView projects.”
Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives (2012, background): “Database methods of loop structure prediction measure the orientation and separation of the backbone segments, flanking the region to be modeled, and then search the PDB for segments of the same length that span a region of similar size and orientation.”
UniProt: the Universal Protein knowledgebase (2004, background): “It contains publicly available protein sequences from many different sources, including Swiss-Prot, TrEMBL, PIR-PSD, EMBL (3), Ensembl (4), IPI (http://www.ebi.ac.uk/ IPI), PDB (5), RefSeq (6), FlyBase (7), WormBase (8), and European, American and Japanese patent ofﬁces.”
Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes (2005, methodology): “Furthermore, topologies were inferred for 13 recently determined X-ray structures of integral membrane proteins in the PDB.(25) For these proteins, the DSSP program(26) was used to determine the secondary structure of the proteins, and topologies were assigned by visual inspection using Rasmol.”
Docking and scoring in virtual screening for drug discovery: methods and applications (2004, background): “jpg" NDATA ITEM> ]> The number of proteins with a known three-dimensional structure is increasing rapidly, and structures produced by structural genomics initiatives are beginning to become publicly availabl”
SMART 6: recent updates and new developments (2008, background): “Information on domain presence in 3D structures has been expanded and includes PDB (17) titles and the basic graphical representation of the structure.”
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. (2004, methodology): “Briefly, the data set contains physical interactions from complex protein structures in the Protein Data Bank (Westbrook et al. 2003), verified interactions from small-scale experiments (Mewes et al. 2000; Xenarios et al. 2002; Bader et al. 2003), and protein pairs from small MIPS catalog complexes…”