留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level

GAO Yue-Dong HUANG Jing-Fei

GAO Yue-Dong, HUANG Jing-Fei. An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level. Zoological Research, 2011, 32(3): 262-266. doi: 10.3724/SP.J.1141.2011.03262
Citation: GAO Yue-Dong, HUANG Jing-Fei. An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level. Zoological Research, 2011, 32(3): 262-266. doi: 10.3724/SP.J.1141.2011.03262

Discovery Studio 2.0的模块扩展及应用:残基水平非键相互作用能量的自动批量计算

doi: 10.3724/SP.J.1141.2011.03262
基金项目: 国家重点基础研究发展计划项目“973”(2009CB941302);国家自然科学基金项目(30470939、30623007);中国科学院基金项目(2007211311091)
详细信息
    作者简介:

    高跃东

    通讯作者:

    黄京飞

  • 中图分类号: Q5-3; Q811.4; TP399

An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level

More Information
    Author Bio:

    GAO Yue-Dong

    Corresponding author: HUANG Jing-Fei
  • 摘要: 非键相互作用对于生物体系中的分子识别和结合过程起着关键作用。然而, 传统的方法并不能在残基水平自动批量计算非键相互作用。近年来, 已经发展了一些方法和工具进行非键相互作用的计算分析。该文研究发展了一种可以自动计算残基间非键相互作用的方法, 即用Perl脚本调用Discovery Studio 2.0 (DS2.0, Accelrys Inc.) 底层模块中的非键相互作用协议, 实现了直接利用命令行批量计算非键相互作用能量, 而无需通过DS2.0的图形界面。该方法扩展了DS2.0的计算模块, 并于近期运用到了复合结构的研究分析中。
  • [1] Ashenhurst JA. 2010. Intermolecular oxidative cross-coupling of arenes [J]. Chem Soc Rev, 39(2): 540-548.Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations [J]. J Comut Chem, 4: 187-217.Hirashima A, Huang H. 2008. Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana [J]. Comput Biol Chem, 32(3): 185-190.McCullagh M, Prytkova T, Tonzani S, Winter ND, Schatz GC. 2008. Modeling self-assembly processes driven by nonbonded interactions in soft materials [J]. J Phys Chem B, 112(34): 10388-10398.Nakashima H, Furukawa K, Kashimura Y, Torimitsu K. 2008. Self-assembly of gold nanorods induced by intermolecular interactions of surface- anchored lipids
    [J]. Langmuir, 24(11): 5654-5658.Pyrkov TV, Ozerov IV, Blitskaia ED, Efremov RG. 2010. Molecular docking: role of intermolecular contacts in formation of complexes of proteins with nucleotides and peptides
    [J]. Bioorg Khim, 36(4): 482-492.Sagui C, Darden TA. 1999. Molecular dynamics simulations of biomolecules: long-range electrostatic effects [J]. Annu Rev Biophys Biomol Struct, 28: 155-179.Shuman S, Lima CD. 2004. The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases [J]. Curr Opin Struct Biol, 14(6): 757-764.Spassov VZ, Yan L. 2008. A fast and accurate computational approach to protein ionization [J]. Protein Sci, 17(11): 1955-1970.Spriggs S, Garyu L, Connor R, Summers MF. 2008. Potential intra- and intermolecular interactions involving the unique-5' region of the HIV-1 5'-UTR [J]. Biochemistry, 47(49): 13064-13073.Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. 2002. The Bioperl toolkit: Perl modules for the life sciences [J]. Genome Res, 12(10): 1611-1618.Sundaram K, Prasad CV. 1982. A program to calculate non-bonded interaction energy in biomolecular aggregates [J]. Comput Programs Biomed, 14(1): 41-46.Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. 2005. GROMACS: fast, flexible, and free [J]. J Comput Chem, 26(16): 1701-1718.Wang LK, Nair PA, Shuman S. 2008. Structure-guided mutational analysis of the OB, HhH, and BRCT domains of Escherichia coli DNA ligase [J]. J Biol Chem, 283(34): 23343-23352.Wang LK, Zhu H, Shuman S. 2009. Structure-guided mutational analysis of the nucleotidyltransferase domain of escherichia coli DNA ligase (LigA) [J]. J Biol Chem, 284(13): 8486-8494.Waters ML. 2002. Aromatic interactions in model systems [J]. Curr Opin Chem Biol, 6(6): 736-741.Weiner PK, Kollman PA. 1981. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions [J]. J Comput Chem, 2: 287-303.
    [4]
     
  • 加载中
计量
  • 文章访问数:  1950
  • HTML全文浏览量:  159
  • PDF下载量:  1906
  • 被引次数: 0
出版历程
  • 收稿日期:  2010-08-05
  • 修回日期:  2011-01-18
  • 刊出日期:  2011-06-22

目录

    /

    返回文章
    返回