Literature DB >> 16090010

Structure optimization by conformational space annealing in an off-lattice protein model.

Seung-Yeon Kim1, Sang Bub Lee, Jooyoung Lee.   

Abstract

The optimization results by conformational space annealing are presented for an off-lattice protein model consisting of hydrophobic and hydrophilic residues in Fibonacci sequences. The ground-state energies found are lower than those reported in the literature. In addition, the ground-state conformations in three dimensions exhibit the important aspect of forming a single hydrophobic core in real proteins. The energy landscape for the population of local minima is also investigated.

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Year:  2005        PMID： 16090010     DOI： 10.1103/PhysRevE.72.011916

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


  9 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.  Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2009-05-21       Impact factor: 3.488

5.  Structure optimization of the two-dimensional off-lattice hydrophobic-hydrophilic model.

Authors:  Jingfa Liu; Shengjun Xue; Duanbing Chen; Huantong Geng; Zhaoxia Liu
Journal:  J Biol Phys       Date:  2009-06-11       Impact factor: 1.365

6.  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

7.  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

8.  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

9.  Non-sequential protein structure alignment by conformational space annealing and local refinement.

Authors:  InSuk Joung; Jong Yun Kim; Keehyoung Joo; Jooyoung Lee
Journal:  PLoS One       Date:  2019-01-30       Impact factor: 3.240
  9 in total

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