Literature DB >> 12271136

Escaping free-energy minima.

Alessandro Laio1, Michele Parrinello.   

Abstract

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

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Year:  2002        PMID: 12271136      PMCID: PMC130499          DOI: 10.1073/pnas.202427399

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  8 in total

1.  Efficient, multiple-range random walk algorithm to calculate the density of states.

Authors:  F Wang; D P Landau
Journal:  Phys Rev Lett       Date:  2001-03-05       Impact factor: 9.161

2.  Reaction coordinates of biomolecular isomerization.

Authors:  P G Bolhuis; C Dellago; D Chandler
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-23       Impact factor: 11.205

3.  Action-derived molecular dynamics in the study of rare events.

Authors:  D Passerone; M Parrinello
Journal:  Phys Rev Lett       Date:  2001-08-17       Impact factor: 9.161

4.  Transition path sampling: throwing ropes over rough mountain passes, in the dark.

Authors:  Peter G Bolhuis; David Chandler; Christoph Dellago; Phillip L Geissler
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

5.  Stochastic relaxation, gibbs distributions, and the bayesian restoration of images.

Authors:  S Geman; D Geman
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  1984-06       Impact factor: 6.226

6.  Optimization by simulated annealing.

Authors:  S Kirkpatrick; C D Gelatt; M P Vecchi
Journal:  Science       Date:  1983-05-13       Impact factor: 47.728

7.  Predicting slow structural transitions in macromolecular systems: Conformational flooding.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1995-09

8.  Local elevation: a method for improving the searching properties of molecular dynamics simulation.

Authors:  T Huber; A E Torda; W F van Gunsteren
Journal:  J Comput Aided Mol Des       Date:  1994-12       Impact factor: 3.686

  8 in total
  747 in total

1.  Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.

Authors:  Victor Ovchinnikov; Martin Karplus
Journal:  J Phys Chem B       Date:  2012-03-28       Impact factor: 2.991

2.  Sampling protein motion and solvent effect during ligand binding.

Authors:  Vittorio Limongelli; Luciana Marinelli; Sandro Cosconati; Concettina La Motta; Stefania Sartini; Laura Mugnaini; Federico Da Settimo; Ettore Novellino; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-11       Impact factor: 11.205

3.  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

4.  Statistical analysis of ion mobility spectrometry. I. Unbiased and guided replica-exchange molecular dynamics.

Authors:  Fabien Chirot; Florent Calvo; Florian Albrieux; Jérôme Lemoine; Yury O Tsybin; Philippe Dugourd
Journal:  J Am Soc Mass Spectrom       Date:  2011-12-01       Impact factor: 3.109

5.  Dominant folding pathways of a WW domain.

Authors:  Silvio A Beccara; Tatjana Škrbić; Roberto Covino; Pietro Faccioli
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-26       Impact factor: 11.205

6.  Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting.

Authors:  Maria-Jesus Olarte; Siyoung Kim; Morris E Sharp; Jessica M J Swanson; Robert V Farese; Tobias C Walther
Journal:  Dev Cell       Date:  2020-07-29       Impact factor: 12.270

Review 7.  Molecular dynamics simulations in photosynthesis.

Authors:  Nicoletta Liguori; Roberta Croce; Siewert J Marrink; Sebastian Thallmair
Journal:  Photosynth Res       Date:  2020-04-15       Impact factor: 3.573

8.  Insight into the folding inhibition of the HIV-1 protease by a small peptide.

Authors:  Massimiliano Bonomi; Francesco L Gervasio; Guido Tiana; Davide Provasi; Ricardo A Broglia; Michele Parrinello
Journal:  Biophys J       Date:  2007-06-15       Impact factor: 4.033

9.  Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations.

Authors:  Dalibor Trapl; Izabela Horvacanin; Vaclav Mareska; Furkan Ozcelik; Gozde Unal; Vojtech Spiwok
Journal:  Front Mol Biosci       Date:  2019-04-18

10.  Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet.

Authors:  Lauren E Buchanan; Emily B Dunkelberger; Huong Q Tran; Pin-Nan Cheng; Chi-Cheng Chiu; Ping Cao; Daniel P Raleigh; Juan J de Pablo; James S Nowick; Martin T Zanni
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-11       Impact factor: 11.205

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