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Molecular Modeling of Transporters: From Low Resolution Cryo-Electron Microscopy Map to Conformational Exploration. The Example of TSPO

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1635)

Abstract

This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to explore its conformational landscape. It combines predictions from up-to-date bioinformatics methods with low-resolution experimental data. It also proposes to examine rapidly the dynamics of the protein using molecular dynamics simulations with a coarse-grained force field. Tools for analyzing these trajectories are suggested as well as those for constructing all-atoms models. Thus, starting from a protein sequence and using free software, the user can get important conformational information, which might improve the knowledge about the protein function.

Key words

3D molecular modeling Coevolution methods Dynamics Coarse-grained models Electron microscopy data 
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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Unité INSERM UMRS1134, Laboratory of Excellence, Institut National de la Transfusion SanguineUniversité Paris-Diderot, Sorbonne Paris Cité, Université de la RéunionParis Cedex 15France

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