IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities.

ABSTRACT: IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dat

SUBMITTER: Kurbatova N 

PROVIDER: S-EPMC3892921 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature