The Protein Data Bank and the challenge of structural genomics

By Helen M. Berman, T. Bhat, Philip E. Bourne, Zukang Feng, Gary Gilliland, H. Weissig, John D. Westbrook. 2000

560 citations recorded by the source corpus.

How researchers see this paper

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

In Molecular Biology

Citations in the corpus

Revealing evolutionary constraints on proteins through sequence analysis (2018, background): “(a) Cartoon representation of the third PDZ domain of the rat postsynaptic density protein 95 from the RSCB PDB [32], (gray: ligand free, 1BFE; blue: ligand bound, 1BE9 (ligand not shown)).”
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins (2012, background): “…the disordered residues are those marked by REMARK465 tag in the experimentally determined protein structures deposited in Protein Data Bank (PDB) [20], which indicates regions with missing coordinates in crystal structures determined by X-ray crystallography or residues with highly variable…”
Protein-protein docking with backbone flexibility. (2007, unknown): “However, the structures of only a small fraction of these potential complexes have been characterized by experimental techniques such as X-ray crystallography, NMR and electron microscopy.(3) Such a gap might be bridged by computational protein–protein docking, which generates a structural model of ”
An interaction-motif-based scoring function for protein-ligand docking (2010, methodology): “Interestingly, while only 28 and 2 protein structures were annotated by PDB [23] as having, respectively, a histidine-triad or a 2-His-1-carboxylate facial triad in the 6,276 protein-ligand complex structures we analyzed, roughly 2% and 5% of these proteins contain NRE-NRE-NRE (on 3 different…”
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”
Intrinsic disorder and functional proteomics. (2007, background): “That is, whereas the number of translated protein sequences has surpassed the 4,000,000 mark, the number of protein structures in PDB is nearing the much lower 40,000 number, corresponding to only ;1% of currently determined protein sequences.”
Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007, methodology): “The predicted structures of the Nterminal regions of Als1 and Als3 were extracted from their larger models, and structures for E-cadherin and N-cadherin were obtained from the Protein Data Bank [62].”
Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases (2007, background): “Synthetic lethality [85,86] þ In vivo Functional association Identification”
The Protein Data Bank and structural genomics (2003, background): “The PDB has been actively involved in various aspects of structural genomics (3), ranging from target tracking to the automation of data deposition from the many steps involved in high throughput structure determination (Fig.”