Dataset Information

PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins.

ABSTRACT: PDBSiteScan is a web-accessible program designed for searching three-dimensional (3D) protein fragments similar in structure to known active, binding and posttranslational modification sites. A collection of known sites we designated as PDBSite was set up by automated processing of the PDB database using the data on site localization in the SITE field. Additionally, protein-protein interaction sites were generated by analysis of atom coordinates in heterocomplexes. The total number of collected sites was more than 8100; they were assigned to more than 80 functional groups. PDBSiteScan provides automated search of the 3D protein fragments whose maximum distance mismatch (MDM) between N, Calpha and C atoms in a fragment and a functional site is not larger than the MDM threshold defined by the user. PDBSiteScan requires perfect matching of amino acids. PDBSiteScan enables recognition of functional sites in tertiary structures of proteins and allows proteins with functional information to be annotated. The program PDBSiteScan is available at http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html.

SUBMITTER: Ivanisenko VA

PROVIDER: S-EPMC441577 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins.

Ivanisenko Vladimir A VA Pintus Sergey S SS Grigorovich Dmitry A DA Kolchanov Nickolay A NA

Nucleic acids research 20040701 Web Server issue

PDBSiteScan is a web-accessible program designed for searching three-dimensional (3D) protein fragments similar in structure to known active, binding and posttranslational modification sites. A collection of known sites we designated as PDBSite was set up by automated processing of the PDB database using the data on site localization in the SITE field. Additionally, protein-protein interaction sites were generated by analysis of atom coordinates in heterocomplexes. The total number of collected ...[more]

PMID: 15215447

Similar Datasets

Project description:Background Analysis of the 3D structures of protein–ligand binding sites can provide valuable insights for drug discovery. Binding site comparison (BSC) studies can be employed to elucidate the function of orphan proteins or to predict the potential for polypharmacology. Many previous binding site analyses only consider binding sites surrounding an experimentally observed bound ligand. Results To encompass potential protein–ligand binding sites that do not have ligands known to bind, we have incorporated fpocket cavity detection software and assessed the impact of this inclusion on BSC performance. Using fpocket, we generated a database of ligand-independent potential binding sites and applied the BSC tool, SiteHopper, to analyze similarity relationships between protein binding sites. We developed a method for clustering potential binding sites using a curated dataset of structures for six therapeutically relevant proteins from diverse protein classes in the protein data bank. Two clustering methods were explored; hierarchical clustering and a density-based method adept at excluding noise and outliers from a dataset. We introduce circular plots to visualize binding site structure space. From the datasets analyzed in this study, we highlight a structural relationship between binding sites of cationic trypsin and prothrombin, protein targets known to bind structurally similar small molecules, exemplifying the potential utility of objectively and holistically mapping binding site space from the structural proteome. Conclusions We present a workflow for the objective mapping of potential protein–ligand binding sites derived from the currently available structural proteome. We show that ligand-independent binding site detection tools can be introduced without excessive penalty on BSC performance. Clustering combined with intuitive visualization tools can be applied to map relationships between the 3D structures of protein binding sites.Graphical abstract Mapping binding site space. Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0180-0) contains supplementary material, which is available to authorized users.

Dataset Information

PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins.

Publications

PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets