ZOOLOGICAL RESEARCH 2011, 32(3) 262-266 DOI:   10.3724/SP.J.1141.2011.03262   ISSN: 0254-5853 CN: 53-1040/Q

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Keywords
Non-bonded energy
Protocol extension
Discovery Studio 2.0
Authors
PubMed

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

GAO Yue-Dong 1,2 , HUANG Jing-Fei 1,3 ,*

1. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China; 2. Graduate School of Chinese Academy of Sciences, Beijing 100039, China; 3. Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, the Chinese Academy of Sciences, Chinese University of Hong Kong, Kunming 650223, China

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  
Received 2010-08-05 Revised 2011-01-18 Online: 2011-06-22 
DOI: 10.3724/SP.J.1141.2011.03262
Fund:
Corresponding Authors: HUANG Jing-Fei
Email: huangjf@mail.kiz.ac.cn
About author: GAO Yue-Dong

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