MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
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DOI：
10.1093/nar/gkh384
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Chen, YZ
中科院分区：
文献类型：
--
作者：
Cao, ZW;Xue, Y;Chen, YZ
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、动力学和功能性质的一种广泛应用的方法。因此，开发一个免费访问的Web服务器，用于计算生物分子的振动和热波动动力学，有利于促进相关的研究。我们已经开发了一个计算蛋白质和核酸的振动简正模和热涨落性质的计算机程序，并将其应用于几项研究。在我们的程序中，振动的简正模计算使用修改的AMBER分子力学力场，和热涨落性质的计算通过自洽谐波近似方法。我们的程序，MoViES（分子振动评估服务器）的网络版本，成立，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，计算的正常模式和热波动键断裂概率与实验结果和其他正常模式的计算结果是一致的。可以在http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl上访问MoviES。
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.