Literature DB >> 20171876

Targeting biomolecular flexibility with metadynamics.

Vanessa Leone1, Fabrizio Marinelli, Paolo Carloni, Michele Parrinello.   

Abstract

Metadynamics calculations allow investigating structure, plasticity, and energetics in a variety of biological processes spanning from molecular docking to protein folding. Recent theoretical developments have led to applications to increasingly complex systems and processes stepping up the biological relevance of the problem solved. Here, after summarizing recent technical advances and applications, we give a perspective of the method as a tool for enzymology and for the prediction of NMR and other spectroscopic data.

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Year:  2010        PMID: 20171876     DOI: 10.1016/j.sbi.2010.01.011

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


  35 in total

1.  Energy landscape of the prion protein helix 1 probed by metadynamics and NMR.

Authors:  Carlo Camilloni; Daniel Schaal; Kristian Schweimer; Stephan Schwarzinger; Alfonso De Simone
Journal:  Biophys J       Date:  2012-01-03       Impact factor: 4.033

Review 2.  Computational methods in drug discovery.

Authors:  Gregory Sliwoski; Sandeepkumar Kothiwale; Jens Meiler; Edward W Lowe
Journal:  Pharmacol Rev       Date:  2013-12-31       Impact factor: 25.468

3.  Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.

Authors:  Wenwei Zheng; Attilio Vittorio Vargiu; Attlio Vittorio Vargiu; Mary A Rohrdanz; Paolo Carloni; Cecilia Clementi
Journal:  J Chem Phys       Date:  2013-10-14       Impact factor: 3.488

4.  Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism.

Authors:  Fabrizio Marinelli
Journal:  Biophys J       Date:  2013-09-03       Impact factor: 4.033

5.  Implementation of Accelerated Molecular Dynamics in NAMD.

Authors:  Yi Wang; Christopher B Harrison; Klaus Schulten; J Andrew McCammon
Journal:  Comput Sci Discov       Date:  2011

6.  Molecular motions in drug design: the coming age of the metadynamics method.

Authors:  Xevi Biarnés; Salvatore Bongarzone; Attilio Vittorio Vargiu; Paolo Carloni; Paolo Ruggerone
Journal:  J Comput Aided Mol Des       Date:  2011-02-17       Impact factor: 3.686

Review 7.  Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution.

Authors:  Alessandro Crnjar; Federico Comitani; Claudio Melis; Carla Molteni
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

8.  EPSP synthase flexibility is determinant to its function: computational molecular dynamics and metadynamics studies.

Authors:  Luís Fernando Saraiva Macedo Timmers; Antônio M S Neto; Rinaldo W Montalvão; Luiz A Basso; Diógenes S Santos; Osmar Norberto de Souza
Journal:  J Mol Model       Date:  2017-06-07       Impact factor: 1.810

9.  Conformational flexibility of human casein kinase catalytic subunit explored by metadynamics.

Authors:  Aurélie Gouron; Anne Milet; Helene Jamet
Journal:  Biophys J       Date:  2014-03-04       Impact factor: 4.033

10.  Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

Authors:  Gabrielle Stetz; Gennady M Verkhivker
Journal:  PLoS One       Date:  2015-11-30       Impact factor: 3.240

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