Literature DB >> 16851755

Assessing the accuracy of metadynamics.

Alessandro Laio1, Antonio Rodriguez-Fortea, Francesco Luigi Gervasio, Matteo Ceccarelli, Michele Parrinello.   

Abstract

Metadynamics is a powerful technique that has been successfully exploited to explore the multidimensional free energy surface of complex polyatomic systems and predict transition mechanisms in very different fields, ranging from chemistry and solid-state physics to biophysics. We here derive an explicit expression for the accuracy of the methodology and provide a way to choose the parameters of the method in order to optimize its performance.

Year:  2005        PMID: 16851755     DOI: 10.1021/jp045424k

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  70 in total

1.  Investigating reaction pathways in rare events simulations of antibiotics diffusion through protein channels.

Authors:  Eric Hajjar; Amit Kumar; Paolo Ruggerone; Matteo Ceccarelli
Journal:  J Mol Model       Date:  2010-11       Impact factor: 1.810

2.  Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems.

Authors:  Lianqing Zheng; Mengen Chen; Wei Yang
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-15       Impact factor: 11.205

3.  Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.

Authors:  Vojtech Spiwok; Blanka Králová; Igor Tvaroska
Journal:  J Mol Model       Date:  2008-07-17       Impact factor: 1.810

4.  Nucleotide-dependent conformational states of actin.

Authors:  Jim Pfaendtner; Davide Branduardi; Michele Parrinello; Thomas D Pollard; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-20       Impact factor: 11.205

5.  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

6.  (Un)Folding mechanisms of the FBP28 WW domain in explicit solvent revealed by multiple rare event simulation methods.

Authors:  Jarek Juraszek; Peter G Bolhuis
Journal:  Biophys J       Date:  2010-02-17       Impact factor: 4.033

7.  Bridging timescales and length scales: from macroscopic flux to the molecular mechanism of antibiotic diffusion through porins.

Authors:  Eric Hajjar; Kozhinjampara R Mahendran; Amit Kumar; Andrey Bessonov; Mircea Petrescu; Helge Weingart; Paolo Ruggerone; Mathias Winterhalter; Matteo Ceccarelli
Journal:  Biophys J       Date:  2010-02-17       Impact factor: 4.033

8.  Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases.

Authors:  Chung F Wong
Journal:  Protein Sci       Date:  2015-06-22       Impact factor: 6.725

9.  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

10.  Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor.

Authors:  Claudio Melis; Giovanni Bussi; Sarah C R Lummis; Carla Molteni
Journal:  J Phys Chem B       Date:  2009-09-03       Impact factor: 2.991

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