Literature DB >> 21804642

Monte Carlo simulations of the HP model (the "Ising model" of protein folding).

Ying Wai Li1, Thomas Wüst, David P Landau.   

Abstract

Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse "transition" to a globule state followed by a second "transition" into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of "transitions". These transitions depend upon the relative interaction strengths and are largely inaccessible to "standard" Monte Carlo methods.

Entities:  

Year:  2011        PMID: 21804642      PMCID: PMC3143505          DOI: 10.1016/j.cpc.2010.12.049

Source DB:  PubMed          Journal:  Comput Phys Commun        ISSN: 0010-4655            Impact factor:   4.390


  13 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.  Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram.

Authors:  F Wang; D P Landau
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2001-10-17

3.  Thermodynamics of lattice heteropolymers.

Authors:  Michael Bachmann; Wolfhard Janke
Journal:  J Chem Phys       Date:  2004-04-08       Impact factor: 3.488

Review 4.  Physics of proteins.

Authors:  Jayanth R Banavar; Amos Maritan
Journal:  Annu Rev Biophys Biomol Struct       Date:  2007

Review 5.  The protein folding problem.

Authors:  Ken A Dill; S Banu Ozkan; M Scott Shell; Thomas R Weikl
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

6.  Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete.

Authors:  B Berger; T Leighton
Journal:  J Comput Biol       Date:  1998       Impact factor: 1.479

7.  Theory for the folding and stability of globular proteins.

Authors:  K A Dill
Journal:  Biochemistry       Date:  1985-03-12       Impact factor: 3.162

8.  Funnels, pathways, and the energy landscape of protein folding: a synthesis.

Authors:  J D Bryngelson; J N Onuchic; N D Socci; P G Wolynes
Journal:  Proteins       Date:  1995-03

9.  Systematic microcanonical analyses of polymer adsorption transitions.

Authors:  Monika Möddel; Wolfhard Janke; Michael Bachmann
Journal:  Phys Chem Chem Phys       Date:  2010-08-06       Impact factor: 3.676

10.  Freezing and collapse of flexible polymers on regular lattices in three dimensions.

Authors:  Thomas Vogel; Michael Bachmann; Wolfhard Janke
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-12-20
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