The RCSB Protein Data Bank: redesigned web site and web services

By Peter W. Rose, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, D. Dimitropoulos, David S. Goodsell, Andreas Prlic, Martha Quesada, Greg B. Quinn, John D. Westbrook and 5 more. 2010

668 citations recorded by the source corpus.

The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Quantitative missense variant effect prediction using large-scale mutagenesis data (2017, positive): “To obtain structural information, we use DSSP (http://www.cmbi.ru.nl/dssp.html) (Kabsch and Sander, 1983) and PDB files from the Protein Data Bank (http://www.rcsb.org/pdb/home/home.do) (Rose et al., 2011).”
The UCSC Genome Browser (2003, neutral): “…the HUGO Gene Nomenclature Committee Database (HGNC; Seal et al., 2011 ), the Cancer Genome Anatomy Project (CGAP; Strausberg et al., 2001 ), PDB ( Rose et al., 2011 ), ModBase ( Pieper et al., 2011 ), InterPro (Hunter et al., 2011), Pfam ( Finn et al., 2010 ), the Stanford SOURCE ( Diehn et al.,…”
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format (2011, background): “The PDBj provides its own data viewer, integrated tools and derived databases in order to facilitate structural biology and bioinformatics research from different perspectives than other members of the wwPDB. PDBj has been engaged in validation of the PDB data description by developing a canonical X”
HMMER web server: interactive sequence similarity searching (2011, background): “Currently, the query sequence can be searched against one of six different target sequence databases: NR (14), UniProtKB (15), SwissProt, PDB (16), UniMes and the environmental division of NR.”
D2P2: database of disordered protein predictions (2012, background): “Much work has been done on producing classification and annotation of known unstructured regions from 3D experimental data found in the PDB (8), DisProt (9) and IDEAL (10) resources.”
TCRmodel: high resolution modeling of T cell receptors from sequence (2018, methodology): “To benchmark the performance of the TCRmodel server, we assembled a set of test cases from recently released TCR structures from the PDB that are nonredundant (containing matching CDR sequences or CDR point mutants) with previously released TCR structures (Supplementary Table S3).”
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA (2012, background): “For a complete picture on the enzyme properties BRENDA includes data from many external sources such as genome sequences [EBI Genomes Server (10), Ensembl database (11)], protein sequences [UniProt databases (12,13)], functional assignments [COG database (14)], molecular pathways [KEGG database (15)”
The RCSB Protein Data Bank: new resources for research and education (2012, methodology): “The PDB is maintained by the members of the Worldwide PDB (wwPDB): RCSB PDB (USA) (1,3), PDB in Europe (PDBe, http://pdbe.org) (4), PDB Japan (PDBj, http://pdbj.org) (5) and BioMagResBank (http:// bmrb.wisc.edu) (6).”
ConoServer: updated content, knowledge, and discovery tools in the conopeptide database (2011, background): “The majority of the sequence and threedimensional structure data are retrieved from publicly available databases, including GenBank (21), UniProtKB (22), the Protein Data Bank (23) and the Biological Magnetic Resonance Bank (24).”
Big Data for Health (2015, background): “resources, such as gene and drug databases [62].”
Ligand placement based on prior structures: the guided ligand-replacement method (2013, methodology): “Thirdly, the RCSB web service (Rose et al., 2011) can be used to query the Chemical Component Dictionary (Henrick et al., 2008) for ligands and their associated structures based on just the ligand code (e.g. ATP).”
AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012, methodology): “PDBderived fragments with greater than 5% sequence identity were excluded in order to treat each target as a novel fold.”
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse (2011, methodology): “PDB (29) is queried monthly for new structures associated with proteins in PSP.”
Prediction of amino acid side chain conformation using a deep neural network (2017, methodology): “generated by using all public structures derived using X-ray crystallography from the Research Collaboratory for Structural Bioinformatics (RCSB) PDB(21, 26), excluding those with a resolution above 1.”
PDBTM: Protein Data Bank of transmembrane proteins after 8 years (2012, methodology): “As a consequence, the proportion of transmembrane and globular proteins in the Protein Data Bank (PDB) (4) database is <2% according to the PDBTM database (5,6).”