Literature DB >> 15903458

Multicanonical study of coarse-grained off-lattice models for folding heteropolymers.

Michael Bachmann1, Handan Arkin, Wolfhard Janke.   

Abstract

We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions of selected sequences with 20 monomers. Another aspect of the investigation was the comparison with the purely hydrophobic homopolymer and the study of general conformational properties induced by the "disorder" in the sequence of a heteropolymer. Furthermore, we applied an optimization algorithm to sequences with up to 55 monomers and compared the global-energy minimum found with lowest-energy states identified within the multicanonical simulation. This was used to find out how reliable the multicanonical method samples the free-energy landscape, in particular for low temperatures.

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Year:  2005        PMID: 15903458     DOI: 10.1103/PhysRevE.71.031906

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  7 in total

1.  Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm.

Authors:  Bai Li; Mu Lin; Qiao Liu; Ya Li; Changjun Zhou
Journal:  J Mol Model       Date:  2015-09-17       Impact factor: 1.810

2.  Heuristic algorithm for off-lattice protein folding problem.

Authors:  Mao Chen; Wen-Qi Huang
Journal:  J Zhejiang Univ Sci B       Date:  2006-01       Impact factor: 3.066

3.  Simulation via direct computation of partition functions.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-09-20

4.  Differential evolution for protein folding optimization based on a three-dimensional AB off-lattice model.

Authors:  Borko Bošković; Janez Brest
Journal:  J Mol Model       Date:  2016-09-30       Impact factor: 1.810

5.  3D protein structure prediction with genetic tabu search algorithm.

Authors:  Xiaolong Zhang; Ting Wang; Huiping Luo; Jack Y Yang; Youping Deng; Jinshan Tang; Mary Qu Yang
Journal:  BMC Syst Biol       Date:  2010-05-28

6.  Protein structure prediction with local adjust tabu search algorithm.

Authors:  Xiaoli Lin; Xiaolong Zhang; Fengli Zhou
Journal:  BMC Bioinformatics       Date:  2014-12-03       Impact factor: 3.169

7.  A quasi-physical algorithm for the structure optimization in an off-lattice protein model.

Authors:  Jing-Fa Liu; Wen-Qi Huang
Journal:  Genomics Proteomics Bioinformatics       Date:  2006-02       Impact factor: 7.691

  7 in total

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