Cao Z W, Xue Y, Han L Y, Xie B, Zhou H, Zheng C J, Lin H H, Chen Y Z
Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W679-85. doi: 10.1093/nar/gkh384.
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.
振动运动和热涨落动力学分析是研究蛋白质和核酸的结构、动力学及功能特性的一种广泛应用的方法。因此，开发一个可免费访问的用于计算生物分子振动和热涨落动力学的网络服务器，有助于推动相关研究。我们已经开发了一个用于计算蛋白质和核酸振动简正模式及热涨落特性的计算机程序，并将其应用于多项研究中。在我们的程序中，振动简正模式通过使用改进的AMBER分子力学力场来计算，热涨落特性则通过自洽谐波近似方法来计算。我们程序的网络版本MoViES（分子振动评估服务器）已搭建完成，以方便使用我们的程序来研究蛋白质和核酸的振动动力学。该软件在选定的蛋白质上进行了测试，结果表明计算得到的简正模式和热涨落键断裂概率与实验结果及其他简正模式计算结果一致。可通过http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl访问MoViES。
