MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
1 Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore, 2 ShangHai Center for Bioinformatics Technology, 100 QinZhou Road, Level 12, ShangHai 200235, People's Republic of China, 3 Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China and 4 Department of Biological Science, National University of Singapore, Blk S3, 14 Science Dr4, Singapore 117543, Singapore
* To whom correspondence should be addressed. Tel: +65 6874 6877; Fax: +65 6774 6756; Email: yzchen{at}cz3.nus.edu.sg
Received February 13, 2004; Revised March 12, 2004; Accepted March 24, 2004
Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. In our program, vibrational normal modes are computed by using modified AMBER molecular mechanics force fields, and thermal fluctuational properties are computed by means of a self-consistent harmonic approximation method. A web version of our program, MoViES (Molecular Vibrations Evaluation Server), was set up to facilitate the use of our program to study vibrational dynamics of proteins and nucleic acids. This software was tested on selected proteins, which show that the computed normal modes and thermal fluctuational bond disruption probabilities are consistent with experimental findings and other normal mode computations. MoViES can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl.
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