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

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(DS 2.0,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。

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.