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高等学校化学研究 ›› 2004, Vol. 20 ›› Issue (5): 572-574.

• Articles • 上一篇    下一篇

A Global Minimization Algorithm for Empirical Contact Potential Functions

WANG Yu-hong, LI Wei   

  1. College of Life Science, Jilin University, Changchun 130023, P. R. China
  • 收稿日期:2003-06-04 出版日期:2004-10-24 发布日期:2011-08-06
  • 基金资助:

    Supported by the National Natural Science Foundation of China(No.30240016).

A Global Minimization Algorithm for Empirical Contact Potential Functions

WANG Yu-hong, LI Wei   

  1. College of Life Science, Jilin University, Changchun 130023, P. R. China
  • Received:2003-06-04 Online:2004-10-24 Published:2011-08-06
  • Supported by:

    Supported by the National Natural Science Foundation of China(No.30240016).

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摘要： Global minimization algorithm is indispensable to solving the protein folding problem based upon thermodynamic hypothesis.Here we propose a pseudo potential function, contact difference (CD), for simulating empirical contact potential functions and testing global minimization algorithm.The present paper covers conformational sampling and global minimization algorithm called BML03, based upon Monte Carlo and simulated annealing, which is able to locate CD's global minimum and refold extended protein structures into ones with root mean square distance(RMSD) as small as 0.03 nm from the native structures.For empirical contact potential functions, these results demonstrate that their global minimization problems may be solvable.

关键词: Global minimization, Contact potential function, Simulated annealing, Monte Carlo simulation, Global minimization, Contact potential function, Simulated annealing, Monte Carlo simulation

Abstract: Global minimization algorithm is indispensable to solving the protein folding problem based upon thermodynamic hypothesis.Here we propose a pseudo potential function, contact difference (CD), for simulating empirical contact potential functions and testing global minimization algorithm.The present paper covers conformational sampling and global minimization algorithm called BML03, based upon Monte Carlo and simulated annealing, which is able to locate CD's global minimum and refold extended protein structures into ones with root mean square distance(RMSD) as small as 0.03 nm from the native structures.For empirical contact potential functions, these results demonstrate that their global minimization problems may be solvable.

Key words: Global minimization, Contact potential function, Simulated annealing, Monte Carlo simulation, Global minimization, Contact potential function, Simulated annealing, Monte Carlo simulation