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Zoological Research
Kunming Institute of Zoology, Chinese Academy of Sciences
ISSN: 2095-8137
Vol. 32, No. 3, 2011, pp. 262-266
Bioline Code: zr11037
Full paper language: Chinese
Document type: Research Article
Document available free of charge

Zoological Research, Vol. 32, No. 3, 2011, pp. 262-266

 en An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level
Gao, Yu-Dong & Huang, Jing-Fei

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.

Keywords
Non-bonded energy; Protocol extension; Discovery Studio 2.0

 
© Copyright 2011 Kunming Institute of Zoology, the Chinese Academy of Sciences
Alternative site location: http://www.zoores.ac.cn/

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