Literature DB >> 9672042

Testing a new Monte Carlo algorithm for protein folding.

U Bastolla1, H Frauenkron, E Gerstner, P Grassberger, W Nadler.   

Abstract

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (PERM) (Grassberger, Phys. Rev. E 56:3682, 1997) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models for lattice heteropolymers, and compare it to published Monte Carlo studies of the properties of particular sequences. In all cases our method is faster than the previous ones, and in several cases we find new minimal energy states. In addition to producing more reliable candidates for ground states, our method gives detailed information about the thermal spectrum and thus allows one to analyze thermodynamic aspects of the folding behavior of arbitrary sequences.

Mesh:

Year:  1998        PMID: 9672042

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  8 in total

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Authors:  G Chikenji; M Kikuchi
Journal:  Proc Natl Acad Sci U S A       Date:  2000-12-19       Impact factor: 11.205

2.  A statistical mechanical method to optimize energy functions for protein folding.

Authors:  U Bastolla; M Vendruscolo; E W Knapp
Journal:  Proc Natl Acad Sci U S A       Date:  2000-04-11       Impact factor: 11.205

3.  Rapid sampling of all-atom peptides using a library-based polymer-growth approach.

Authors:  Artem B Mamonov; Xin Zhang; Daniel M Zuckerman
Journal:  J Comput Chem       Date:  2010-08-23       Impact factor: 3.376

4.  Absolute free energies estimated by combining precalculated molecular fragment libraries.

Authors:  Xin Zhang; Artem B Mamonov; Daniel M Zuckerman
Journal:  J Comput Chem       Date:  2009-08       Impact factor: 3.376

5.  A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank.

Authors:  Ugo Bastolla; Markus Porto; H Eduardo Roman; Michele Vendruscolo
Journal:  BMC Evol Biol       Date:  2006-05-31       Impact factor: 3.260

6.  An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem.

Authors:  Alena Shmygelska; Holger H Hoos
Journal:  BMC Bioinformatics       Date:  2005-02-14       Impact factor: 3.169

7.  A Novel Framework for Ab Initio Coarse Protein Structure Prediction.

Authors:  Sandhya Parasnath Dubey; S Balaji; N Gopalakrishna Kini; M Sathish Kumar
Journal:  Adv Bioinformatics       Date:  2018-06-20

8.  A replica exchange Monte Carlo algorithm for protein folding in the HP model.

Authors:  Chris Thachuk; Alena Shmygelska; Holger H Hoos
Journal:  BMC Bioinformatics       Date:  2007-09-17       Impact factor: 3.169

  8 in total

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