Literature DB >> 26716577

New generation of elastic network models.

José Ramón López-Blanco1, Pablo Chacón2.   

Abstract

The intrinsic flexibility of proteins and nucleic acids can be grasped from remarkably simple mechanical models of particles connected by springs. In recent decades, Elastic Network Models (ENMs) combined with Normal Model Analysis widely confirmed their ability to predict biologically relevant motions of biomolecules and soon became a popular methodology to reveal large-scale dynamics in multiple structural biology scenarios. The simplicity, robustness, low computational cost, and relatively high accuracy are the reasons behind the success of ENMs. This review focuses on recent advances in the development and application of ENMs, paying particular attention to combinations with experimental data. Successful application scenarios include large macromolecular machines, structural refinement, docking, and evolutionary conservation.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Mesh:

Substances:

Year:  2015        PMID: 26716577     DOI: 10.1016/j.sbi.2015.11.013

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  20 in total

Review 1.  Advances in coarse-grained modeling of macromolecular complexes.

Authors:  Alexander J Pak; Gregory A Voth
Journal:  Curr Opin Struct Biol       Date:  2018-11-30       Impact factor: 6.809

2.  Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.

Authors:  Sophie Sacquin-Mora
Journal:  J R Soc Interface       Date:  2019-07-10       Impact factor: 4.118

Review 3.  X-ray Scattering Studies of Protein Structural Dynamics.

Authors:  Steve P Meisburger; William C Thomas; Maxwell B Watkins; Nozomi Ando
Journal:  Chem Rev       Date:  2017-05-30       Impact factor: 60.622

4.  Minimum action principle and shape dynamics.

Authors:  Patrice Koehl
Journal:  J R Soc Interface       Date:  2017-05       Impact factor: 4.118

5.  Allosteric Modulation of Intact γ-Secretase Structural Dynamics.

Authors:  Ji Young Lee; Zhiwei Feng; Xiang-Qun Xie; Ivet Bahar
Journal:  Biophys J       Date:  2017-12-19       Impact factor: 4.033

6.  Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.

Authors:  Didier Devaurs; Malvina Papanastasiou; Dinler A Antunes; Jayvee R Abella; Mark Moll; Daniel Ricklin; John D Lambris; Lydia E Kavraki
Journal:  Int J Comput Biol Drug Des       Date:  2018-03-24

7.  Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.

Authors:  Mathieu Fossépré; Laurence Leherte; Aatto Laaksonen; Daniel P Vercauteren
Journal:  J Mol Model       Date:  2016-08-26       Impact factor: 1.810

8.  Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids.

Authors:  Yin-Chen Hsieh; Frédéric Poitevin; Marc Delarue; Patrice Koehl
Journal:  Front Mol Biosci       Date:  2016-12-27

9.  Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.

Authors:  Didier Devaurs; Dinler A Antunes; Malvina Papanastasiou; Mark Moll; Daniel Ricklin; John D Lambris; Lydia E Kavraki
Journal:  Front Mol Biosci       Date:  2017-03-10

10.  Elastic network model of learned maintained contacts to predict protein motion.

Authors:  Ines Putz; Oliver Brock
Journal:  PLoS One       Date:  2017-08-30       Impact factor: 3.240

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.