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Performance of a docking/molecular dynamics protocol for virtual screening of nutlin-class inhibitors of Mdmx.

ABSTRACT: A virtual screening protocol involving docking and molecular dynamics has been tested against the results of fluorescence polarization assays testing the potency of a series of compounds of the nutlin class for inhibition of the interaction between p53 and Mdmx, an interaction identified as a driver of certain cancers. The protocol uses a standard docking method (AutoDock) with a cutoff based on the AutoDock score (ADscore), followed by molecular dynamics simulation with a cutoff based on root-mean-square-deviation (RMSD) from the docked pose. An analysis of the experimental and computational results shows modest performance of ADscore alone, but dramatically improved performance when RMSD is also used.

SUBMITTER: Bharatham N

PROVIDER: S-EPMC5508530 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Performance of a docking/molecular dynamics protocol for virtual screening of nutlin-class inhibitors of Mdmx.

Bharatham Nagakumar N Finch Kristin E KE Min Jaeki J Mayasundari Anand A Dyer Michael A MA Guy R Kiplin RK Bashford Donald D

Journal of molecular graphics & modelling 20170224

A virtual screening protocol involving docking and molecular dynamics has been tested against the results of fluorescence polarization assays testing the potency of a series of compounds of the nutlin class for inhibition of the interaction between p53 and Mdmx, an interaction identified as a driver of certain cancers. The protocol uses a standard docking method (AutoDock) with a cutoff based on the AutoDock score (ADscore), followed by molecular dynamics simulation with a cutoff based on root-m ...[more]

PMID: 28351017

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