A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit)
| Autor: | Mauricio G. S. Costa, Catherine Vénien-Bryan, David Perahia, Charline Fagnen |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Physics
010304 chemical physics Protein Conformation Cryo-electron microscopy General Chemical Engineering Cryoelectron Microscopy General Chemistry Molecular Dynamics Simulation Library and Information Sciences 01 natural sciences Molecular physics 0104 chemical sciences Computer Science Applications Characterization (materials science) 010404 medicinal & biomolecular chemistry Molecular dynamics Normal mode Excited state 0103 physical sciences sense organs |
| Zdroj: | Journal of Chemical Information and Modeling. 60:2419-2423 |
| ISSN: | 1549-960X 1549-9596 |
| DOI: | 10.1021/acs.jcim.9b01148 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|