Premium
Classification of Binding Site Conformations of Protein Tyrosine Phosphatase 1B
Author(s) -
Tanchuk Vsevolod Yu.,
Tanin Volodymyr O.,
Vovk Andriy I.
Publication year - 2012
Publication title -
chemical biology and drug design
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.59
H-Index - 77
eISSN - 1747-0285
pISSN - 1747-0277
DOI - 10.1111/j.1747-0285.2012.01370.x
Subject(s) - protein tyrosine phosphatase , protein data bank , cluster analysis , tyrosine , dusp6 , enzyme , binding site , biochemistry , chemistry , phosphatase , centroid , computational biology , protein structure , biology , protein phosphatase 2 , computer science , artificial intelligence
Hundred and two binding sites from 91 Protein Data Bank files for protein tyrosine phosphatase 1B with different ligands have been compared. It was found that they can be divided into five clusters. Additional clusters were formed by the unliganded and oxidized enzyme. The centroids of the clusters can be used as starting points for further studies of enzyme‐inhibitor interaction by computer simulations. A special software tool has been created for the investigation of protein tyrosine phosphatase 1B and other enzymes. It performs multiple comparisons of selected parts of Protein Data Bank files, as well as further clustering, and determines mobility of separate residues.