Publication:
Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical monte carlo simulations

Placeholder

Departments

School / College / Institute

Program

KU-Authors

KU Authors

Co-Authors

Marrone, Tami J.
Hodge, C. Nicholas
Chang, Chong-Hwan
McCammon, J. Andrew

Publication Date

Language

Embargo Status

Journal Title

Journal ISSN

Volume Title

Alternative Title

Abstract

We examine the water solvation of the complex of the inhibitors DMP323 and A76928 bound to HIV-1 protease through grand canonical Monte Carlo simulations, and demonstrate the ability of this method to reproduce crystal waters and effectively predict water positions not seen in the DMP323 or A76928 structures. The simulation method is useful for identifying structurally important waters that may not be resolved in the crystal structures. It can also be used to identify water positions around a putative drug candidate docked into a binding pocket. Knowledge of these water positions may be useful in designing drugs to utilize them as bridging groups or displace them in the binding pocket. In addition, the method should be useful in finding water sites in homology models of enzymes for which crystal structures are unavailable.

Source

Publisher

Cambridge Univ Press

Subject

Biochemistry, Molecular Biology

Citation

Has Part

Source

Protein Science

Book Series Title

Edition

DOI

10.1002/pro.5560070305

item.page.datauri

Link

Rights

Copyrights Note

Endorsement

Review

Supplemented By

Referenced By

0

Views

0

Downloads

View PlumX Details