Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities.

ABSTRACT: A computational docking strategy using multiple conformations of the target protein is discussed and evaluated. A series of low molecular weight, competitive, nonpeptide protein tyrosine phosphatase inhibitors are considered for which the x-ray crystallographic structures in complex with protein tyrosine phosphatase 1B (PTP1B) are known. To obtain a quantitative measure of the impact of conformational changes induced by the inhibitors, these were docked to the active site region of various structures of PTP1B using the docking program FlexX. Firstly, the inhibitors were docked to a PTP1B crystal structure cocrystallized with a hexapeptide. The estimated binding energies for various docking modes as well as the RMS differences between the docked compounds and the crystallographic structure

SUBMITTER: Frimurer TM 

PROVIDER: S-EPMC1302794 | biostudies-literature | 2003 Apr

REPOSITORIES: biostudies-literature