PDBSite: a database of the 3D structure of protein functional sites

Abstract

The PDBSite database provides comprehensive structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein–protein, protein–DNA and protein–RNA interactions) in the Protein Data Bank (PDB). The PDBSite is available online at http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/. It consists of functional sites extracted from PDB using the SITE records and of an additional set containing the protein interaction sites inferred from the contact residues in heterocomplexes. The PDBSite was set up by automated processing of the PDB. The PDBSite database can be queried through the functional description and the structural characteristics of the site and its environment. The PDBSite is integrated with the PDBSiteScan tool allowing structural comparisons of a protein against the functional sites. The PDBSite enables the recognition of functional sites in protein tertiary structures, providing annotation of function through structure. The PDBSite is updated after each new PDB release.

Computational chemistry study of 3D‐structure‐function relationships for enzymes based on Markov models for protein electrostatic, HINT, and van der Waals potentials

“…All the PDB files with the 3D protein structures 14 and their classification into enzymes or nonenzymes were taken from the literature. 4 The aforementioned descriptors were subsequently used to carry out a LDA with a random training subset of proteins to classify each one of them as enzyme or nonenzyme.…”

“…All the PDB files with the 3D protein structures 14 and their classification into enzymes or nonenzymes were taken from the literature. 3 Before collecting the PDB files we perform the calculation of the electrostatic potentials, electrostatic entropy, and electrostatic spectral moments as well as vdW potentials, vdW entropy, vdW spectral moments, HINT potentials, HINT entropy, and HINT spectral moments.…”

Exploring protein–ligand recognition with Binding MOAD

“…The data points in black squares are from complexes with K d data, and gray diamonds are used for complexes with K i or IC 50 data. [11,15,25,32,33,[41][42][43][44][45][46][47][48][49][50][51][52][53][54][55], but now, we will be able to add another layer of depth to such studies. There is more to binding affinity than just burying a ligand inside a protein, and all of the complex issues that go into creating an effective scoring function [56] will need to be considered in our analyses.…”

“…Patterns of valid versus invalid ligands of both types should help current efforts in the field to identify binding sites in apo structures. At this time, groups are focusing on the analysis of occupied versus unoccupied pockets and having good success [11,32,33,[41][42][43][44][45][46][47][48][49], but the methods could be further refined with data on the invalid ligands identified within Binding MOAD.…”

Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB)

“…The presence of transmembrane helices was predicted by SOSUI (Hirokawa et al, 1998) and TMHMM (Krogh et al, 2001). Protein 3D-structures were assigned by the Genome to Protein structure and function (GTOP) pipeline (Kawabata et al, 2002), where reverse PSI-BLAST, a variant of the PSI-BLAST algorithm (Altschul et al, 1997) is used for searching of the amino acid sequences derived from the H-Inv cDNA against the PDB database (Ivanisenko et al, 2005).…”