Literature DB >> 21804033

The social network (of protein conformations).

John D Chodera1, Vijay S Pande.   

Abstract

Year:  2011        PMID： 21804033      PMCID： PMC3156194          DOI： 10.1073/pnas.1109571108

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


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  17 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.  The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain.

Authors:  C B ANFINSEN; E HABER; M SELA; F H WHITE
Journal:  Proc Natl Acad Sci U S A       Date:  1961-09-15       Impact factor: 11.205

3.  Escaping free-energy minima.

Authors:  Alessandro Laio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-23       Impact factor: 11.205

4.  The protein folding network.

Authors:  Francesco Rao; Amedeo Caflisch
Journal:  J Mol Biol       Date:  2004-09-03       Impact factor: 5.469

5.  Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction.

Authors:  Payel Das; Mark Moll; Hernán Stamati; Lydia E Kavraki; Cecilia Clementi
Journal:  Proc Natl Acad Sci U S A       Date:  2006-06-19       Impact factor: 11.205

6.  Reactive flux and folding pathways in network models of coarse-grained protein dynamics.

Authors:  Alexander Berezhkovskii; Gerhard Hummer; Attila Szabo
Journal:  J Chem Phys       Date:  2009-05-28       Impact factor: 3.488

7.  From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map.

Authors:  Michele Ceriotti; Gareth A Tribello; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2011-07-05       Impact factor: 11.205

8.  Determination of reaction coordinates via locally scaled diffusion map.

Authors:  Mary A Rohrdanz; Wenwei Zheng; Mauro Maggioni; Cecilia Clementi
Journal:  J Chem Phys       Date:  2011-03-28       Impact factor: 3.488

Review 9.  Everything you wanted to know about Markov State Models but were afraid to ask.

Authors:  Vijay S Pande; Kyle Beauchamp; Gregory R Bowman
Journal:  Methods       Date:  2010-06-04       Impact factor: 3.608

10.  Calculation of the free energy and cooperativity of protein folding.

Authors:  Alex Kentsis; Tatyana Gindin; Mihaly Mezei; Roman Osman
Journal:  PLoS One       Date:  2007-05-16       Impact factor: 3.240
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  3 in total

1.  Approximating frustration scores in complex networks via perturbed Laplacian spectra.

Authors:  Andrej J Savol; Chakra S Chennubhotla
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2015-12-04

Review 2.  Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations.

Authors:  Nina Pastor; Carlos Amero
Journal:  Front Plant Sci       Date:  2015-05-05       Impact factor: 5.753

3.  Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins.

Authors:  Andrej J Savol; Chakra S Chennubhotla
Journal:  J Chem Theory Comput       Date:  2014-06-13       Impact factor: 6.006
  3 in total

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