Literature DB >> 16489726

Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

Bernd Ensing1, Marco De Vivo, Zhiwei Liu, Preston Moore, Michael L Klein.   

Abstract

The metadynamics or hills method is a relatively new molecular dynamics technique aimed to enhance the sampling of separated regions in phase space and map out the underlying free energy landscape as a function of a small number of order parameters or collective variables. The high efficiency allows for the application of metadynamics in combination with first principles dynamics methods, in particular with Car-Parrinello molecular dynamics, to study processes in which changes in the electronic structure play a dominant role, such as chemical reactions. The option to choose several independent collective variables is important to tackle complex and concerted transformations that lack an obvious a priori choice for a single reaction coordinate. In this Account, we discuss the role of metadynamics in the search of transition states, local minima, reaction paths, free energy profiles, and reaction coordinates among a growing list of alternative methods.

Entities:  

Year:  2006        PMID: 16489726     DOI: 10.1021/ar040198i

Source DB:  PubMed          Journal:  Acc Chem Res        ISSN: 0001-4842            Impact factor:   22.384


  46 in total

1.  Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins.

Authors:  Fabrizio Marinelli; Sonja I Kuhlmann; Ernst Grell; Hans-Jörg Kunte; Christine Ziegler; José D Faraldo-Gómez
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-14       Impact factor: 11.205

2.  Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

Authors:  Jerome P Nilmeier; Gavin E Crooks; David D L Minh; John D Chodera
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-24       Impact factor: 11.205

3.  Computational molecular biology approaches to ligand-target interactions.

Authors:  Paola Lupieri; Chuong Ha Hung Nguyen; Zhaleh Ghaemi Bafghi; Alejandro Giorgetti; Paolo Carloni
Journal:  HFSP J       Date:  2009-03-10

4.  Multiscale methods for computational RNA enzymology.

Authors:  Maria T Panteva; Thakshila Dissanayake; Haoyuan Chen; Brian K Radak; Erich R Kuechler; George M Giambaşu; Tai-Sung Lee; Darrin M York
Journal:  Methods Enzymol       Date:  2015-01-22       Impact factor: 1.600

5.  Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations.

Authors:  Parag Mukhopadhyay; Gérard Zuber; David N Beratan
Journal:  Biophys J       Date:  2008-09-19       Impact factor: 4.033

6.  Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulations.

Authors:  Han Zheng; Yingkai Zhang
Journal:  J Chem Phys       Date:  2008-05-28       Impact factor: 3.488

7.  Introducing sampling entropy in repository based adaptive umbrella sampling.

Authors:  Han Zheng; Yingkai Zhang
Journal:  J Chem Phys       Date:  2009-12-07       Impact factor: 3.488

8.  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

9.  Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities.

Authors:  Konstantinos D Vogiatzis; Mikhail V Polynski; Justin K Kirkland; Jacob Townsend; Ali Hashemi; Chong Liu; Evgeny A Pidko
Journal:  Chem Rev       Date:  2018-10-30       Impact factor: 60.622

Review 10.  Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.

Authors:  Shina C L Kamerlin; Maciej Haranczyk; Arieh Warshel
Journal:  J Phys Chem B       Date:  2009-02-05       Impact factor: 2.991

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