A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit)

被引：18
|
作者：
Costa, Mauricio G. S. [1 ,2 ,3 ]
Fagnen, Charline [2 ,3 ]
Venien-Bryan, Catherine [2 ]
Perahia, David [3 ]
机构：
[1] Fundacao Oswaldo Cruz, Programa Computacao Cient, Educ Informacao & Comunicacao, BR-21040900 Rio De Janeiro, Brazil
[2] Sorbonne Univ, Museum Natl Hist Nat, CNRS, UMR 7590,IMPMC, F-75005 Paris, France
[3] CNRS, Ecole Normale Super Paris Saclay, Lab Biol & Pharmacol Appl, 61 Av President Wilson, F-94235 Cachan, France
来源：
JOURNAL OF CHEMICAL INFORMATION AND MODELING | 2020年 / 60卷 / 05期
关键词：
LOW-RESOLUTION; PROTEIN; SIMULATIONS;
D O I：
10.1021/acs.jcim.9b01148
中图分类号：
R914 [药物化学];
学科分类号：
100701 ;
摘要：
Previous studies demonstrated the efficiency of the Molecular Dynamics with excited Normal Modes (MDeNM) method on the characterization of large structural changes at a low computational cost. We present here MDeNM-EMfit, an extension of the original method designed to the flexible fit of structures into cryo-EM maps. Here, instead of a uniform exploration of the collective motions described by normal modes, sampling is directed toward conformations with increased correlations with the experimental map. Future perspectives to improve the accuracy of fitting and speed of calculations are discussed in light of the results.
引用
收藏
页码：2419 / 2423
页数：5
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