Literature DB >> 32622329

Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.

James M Krieger1, Pemra Doruker1, Ana Ligia Scott2, David Perahia3, Ivet Bahar4.   

Abstract

With the explosion of normal mode analyses (NMAs) based on elastic network models (ENMs) in the last decade, and the proven precision of MD simulations for visualizing interactions at atomic scale, many hybrid methods have been proposed in recent years. These aim at exploiting the best of both worlds: the atomic precision of MD that often fall short of exploring time and length scales of biological interest, and the capability of ENM-NMA to predict the cooperative and often functional rearrangements of large structures and assemblies, albeit at low resolution. We present an overview of recent progress in the field with examples of successful applications highlighting the utility of such hybrid methods and pointing to emerging future directions guided by advances in experimental characterization of biomolecular systems structure and dynamics.
Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.

Entities:  

Year:  2020        PMID: 32622329      PMCID: PMC7666066          DOI: 10.1016/j.sbi.2020.05.013

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


  68 in total

1.  Manipulation of conformational change in proteins by single-residue perturbations.

Authors:  C Atilgan; Z N Gerek; S B Ozkan; A R Atilgan
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2.  Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening.

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Authors:  Hongchun Li; Yuan-Yu Chang; Ji Young Lee; Ivet Bahar; Lee-Wei Yang
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

Review 4.  Principles for Integrative Structural Biology Studies.

Authors:  Michael P Rout; Andrej Sali
Journal:  Cell       Date:  2019-05-30       Impact factor: 41.582

5.  Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

Authors:  Katja Ostermeir; Martin Zacharias
Journal:  Proteins       Date:  2014-10-10

6.  Hybrid Electron Microscopy Normal Mode Analysis with Scipion.

Authors:  Mohamad Harastani; Carlos Oscar S Sorzano; Slavica Jonić
Journal:  Protein Sci       Date:  2019-11-20       Impact factor: 6.725

7.  BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures.

Authors:  Ashini Bolia; Z Nevin Gerek; S Banu Ozkan
Journal:  J Chem Inf Model       Date:  2014-03-04       Impact factor: 4.956

8.  Binding of phenothiazines into allosteric hydrophobic pocket of human thioredoxin 1.

Authors:  Eric Allison Philot; David da Mata Lopes; Aryane Tofanello de Souza; Antônio Sérgio Kimus Braz; Iseli Lourenço Nantes; Tiago Rodrigues; David Perahia; Maria A Miteva; Luis Paulo Barbour Scott
Journal:  Eur Biophys J       Date:  2016-01-28       Impact factor: 1.733

9.  Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.

Authors:  Zeynep Kurkcuoglu; Alexandre M J J Bonvin
Journal:  Proteins       Date:  2019-09-03

10.  DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.

Authors:  Carlos Hm Rodrigues; Douglas Ev Pires; David B Ascher
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

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  8 in total

1.  Revealing the activation mechanism of autoinhibited RalF by integrated simulation and experimental approaches.

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2.  State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.

Authors:  Yan Zhang; James Krieger; Karolina Mikulska-Ruminska; Burak Kaynak; Carlos Oscar S Sorzano; José-María Carazo; Jianhua Xing; Ivet Bahar
Journal:  Prog Biophys Mol Biol       Date:  2020-08-28       Impact factor: 3.667

Review 3.  Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: lessons from the pandemic and preparing for future health crises.

Authors:  Natesh Singh; Bruno O Villoutreix
Journal:  Comput Struct Biotechnol J       Date:  2021-04-26       Impact factor: 7.271

4.  Editorial: Understanding Protein Dynamics, Binding and Allostery for Drug Design.

Authors:  Guang Hu; Pemra Doruker; Hongchun Li; Ebru Demet Akten
Journal:  Front Mol Biosci       Date:  2021-04-21

5.  Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials.

Authors:  David Herreros; Roy R Lederman; James Krieger; Amaya Jiménez-Moreno; Marta Martínez; David Myška; David Strelak; Jiri Filipovic; Ivet Bahar; Jose Maria Carazo; Carlos Oscar S Sanchez
Journal:  IUCrJ       Date:  2021-10-14       Impact factor: 4.769

6.  Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.

Authors:  Burak T Kaynak; James M Krieger; Balint Dudas; Zakaria L Dahmani; Mauricio G S Costa; Erika Balog; Ana Ligia Scott; Pemra Doruker; David Perahia; Ivet Bahar
Journal:  Front Mol Biosci       Date:  2022-02-04

Review 7.  Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.

Authors:  James Michael Krieger; Carlos Oscar S Sorzano; Jose Maria Carazo; Ivet Bahar
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-03-16       Impact factor: 7.652

8.  Docking-based long timescale simulation of cell-size protein systems at atomic resolution.

Authors:  Ilya A Vakser; Sergei Grudinin; Nathan W Jenkins; Petras J Kundrotas; Eric J Deeds
Journal:  Proc Natl Acad Sci U S A       Date:  2022-10-03       Impact factor: 12.779

  8 in total

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