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
An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level
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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。Abstract: Non-bonded interaction forces play crucial roles in molecular recognition and binding in biological systems.However, it is difficult for traditional methods to automatically calculate and batch the non-bonded energy at the residue level. In recent years, many studies have focused on non-bonded interactions and developed tools to calculate and analyze such interactions. In this study, we present a highly automated approach for the calculation of non-bonded energy. Our strategy invoked protocols relevant to non-bonded interactions within Discovery Studio 2.0 (DS2.0, Accelrys Inc.) bottom module using Perl script, and determined the direct command line operation of calculating non-bonded interaction energy batches without accessing the graphical interface of DS. This approach extended the DS2.0 module and was applied to a recent study of complex structure analysis.