The RCSB Protein Data Bank: new resources for research and education

By Peter W. Rose, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, D. Dimitropoulos, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, Andreas Prlic, Martha Quesada and 7 more. Nucleic Acids Res., 2012

532 citations recorded by the source corpus.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher’s PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/863ecf1e810e79608ffb167ea5de91b0e1936c25

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Citations in the corpus

The carbohydrate-active enzymes database (CAZy) in 2013 (2013, background): “Until September 2013, the only information available in the structure pages of CAZy was the accession and macromolecule chain name(s) in the PDB (http:// www.rcsb.org) (19).”
Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics (2015, unknown): “To distinguish the characteristics of FG-Nups, a collection of 1,138 FG-Nups and two random sets of 1,138 structured proteins from Protein Data Bank (PDB) [38] are compared.”
The Transporter Classification Database (2013, unknown): “In addition to the search option under the search tab, one can search TCDB from a search box on the main page using single or multiple terms including TC ID#, key word, protein name or abbreviation, organismal source, author name, UniProt accession number, PDB ID number, associated disease, referenc”
Evaluation of predictions in the CASP10 model refinement category (2013, methodology): “The Protein Structure Prediction Center estimated how well submitted 3D models fitted the corresponding target structures, as well as other stereochemical features observed in the PDB. 24 All structural alignments were calculated with LGA21 in sequence-dependent mode, while model stereochemistry was”
The RCSB protein data bank: integrative view of protein, gene and 3D structural information (2016, unknown): “org) (2,7,8) offers multiple tools for structure query, browsing, analysis and molecular visualization.”
Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology (2013, methodology): “Considering structure availability and binding site certainty, we selectively downloaded a set of co-crystallized kinase structures from the PDB database [31] (Materials and Methods).”
NGL Viewer: a web application for molecular visualization (2015, methodology): “Specifically, integration of browser-based visualizations simplifies access to results of structure-related calculations from web tools (3,4) and allows for quick depiction of entries in online structural databases (5–7).”
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education (2014, methodology): “It has grown to more than 104 000 entries, a 20% increase in just 2 years (2).”
PATRIC, the bacterial bioinformatics database and analysis resource (2013, background): “Currently, there are more than 33 000 experimentally solved bacterial protein structures available in various public data repositories such as the PDB (18) and NCBI MMDB (19).”
IMGT®, the international ImMunoGeneTics information system® 25 years on (2014, methodology): “‘IMGT numbering comparison’ provides, per domain, the IMGT DOMAIN numbering by comparison with the PDB numbering, and the residue (3-letter and 1-letter names), which allows standardized IMGT representations using generic tools.”
DrugBank 4.0: shedding new light on drug metabolism (2013, background): “In addition, DrugBank now offers comprehensive, colorful, manually drawn interactive drug metabolism pathways [using the SMPDB pathway model (13)] for >50 drugs.”
MMDB and VAST+: tracking structural similarities between macromolecular complexes (2013, methodology): “At this point, the VAST-search service, which accepts 3D structure data uploaded in PDB-format, remains unchanged, and presents similar structures in the Original VAST format (Table 1).”
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12 (2018, background): “…that CAMEO conducts fully automated prediction assessments based on the pre-release of sequences[12] of those structures which are going to be published by the PDB Protein Data Bank[13] the following Wednesday, i.e. the evaluation is based on blind predictions of unpublished 3D structures.”