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ZOOLOGICAL RESEARCH    2011, Vol. 32 Issue (3) : 262-266     DOI: 10.3724/SP.J.1141.2011.03262
Articles |
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
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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     
PACS:  Q5-3  
  Q811.4  
  TP399  
Corresponding Authors: HUANG Jing-Fei   
About author: GAO Yue-Dong
Issue Date: 22 June 2011
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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[J]. ZOOLOGICAL RESEARCH,2011, 32(3): 262-266.
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http://www.zoores.ac.cn/EN/10.3724/SP.J.1141.2011.03262     OR     http://www.zoores.ac.cn/EN/Y2011/V32/I3/262
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