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

Abstract

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.

A WXW Motif Is Required for the Anticancer Activity of the TAT-RasGAP317–326 Peptide

“…The DLC1 GAP domain (Protein Data Bank (PDB) ID: 3KUQ (22,23)) was used as the receptor and the RasGAP SH3 domain (PDB ID: 2J05 (24)) as the ligand. The receptor and ligand binding sites were not imposed, and no additional constraint was applied during the docking.…”

Calprotectin Complex Interactions with Phytoquinolines and New Target Binding Alternates Calprotectin complex and Phytoquinolines

“…29 Comparative analysis, with structures of various substitutes of quinoline-3-carboxamides, is undertaken, to determine interaction with S100 member proteins. These carboxamide derivatives exhibited optimal binding, with the S100 member targets.…”

Genome-wide inference of protein interaction network and its application to the study of crosstalk in Arabidopsis abscisic acid signaling

“…A total of 90,424 and 88,999 structures involving multiple organisms were available in the PDB (Rose et al, 2013) and Proteins, Interfaces, Structures, and Assemblies databases, respectively. The chain-chain binary interface and the binding sites of protein complexes were generated in the PIBASE software package with an interatomic distance cutoff of 6.05 Å (Davis and Sali, 2005).…”

“…Recently, computational methods using structural information for PPI prediction have gained much attention due to the rapid growth of the Protein Data Bank (PDB; Rose et al, 2013). Protein docking is a promising method for discovering protein interactions that is based on three-dimensional structural information, but it remains a challenging and computationally demanding task to predict PPIs on a genome-wide scale (Wass et al, 2011).…”