Author: Glantz-Gashai, Yitav; Meirson, Tomer; Reuveni, Eli; Samson, Abraham O
Title: Virtual screening for potential inhibitors of Mcl-1 conformations sampled by normal modes, molecular dynamics, and nuclear magnetic resonance Document date: 2017_6_19
ID: 47srfqzl_4
Snippet: To assist virtual screening, several studies have used molecular dynamics (MD) simulations. 20 MD simulation is a well-established method for understanding protein dynamics. In most cases, MD simulations provide snapshots that improve virtual screening predictive power over known crystal structures, possibly due to sampling more relevant conformations. Furthermore, unrestrained MD simulations can move conformations previously not amenable to dock.....
Document: To assist virtual screening, several studies have used molecular dynamics (MD) simulations. 20 MD simulation is a well-established method for understanding protein dynamics. In most cases, MD simulations provide snapshots that improve virtual screening predictive power over known crystal structures, possibly due to sampling more relevant conformations. Furthermore, unrestrained MD simulations can move conformations previously not amenable to docking into the predictive range. 21 To assist virtual screening, several studies have also used normal mode analysis (NMA). 22 NMA is one of the standard techniques for studying long-time dynamics and, in particular, low-frequency motions. 23 In contrast to MD, NMA provides an analytical and fully detailed description of the dynamics around a local energy minimum, 24, 25 and the conformation ensemble is generated by perturbing the initial structure along a set of relevant low-frequency normal modes.
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