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

GAO Yue-Dong; HUANG Jing-Fei

doi:10.3724/SP.J.1141.2011.03262

Volume 32 Issue 3

May 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. Zoological Research, 2011, 32(3): 262-266. doi: 10.3724/SP.J.1141.2011.03262

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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. Zoological Research, 2011, 32(3): 262-266. doi: 10.3724/SP.J.1141.2011.03262

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

doi: 10.3724/SP.J.1141.2011.03262

GAO Yue-Dong,
HUANG Jing-Fei^{1,3 ,*
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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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Author Bio:
GAO Yue-Dong
Corresponding author: HUANG Jing-Fei
Received Date: 2010-08-05
Rev Recd Date: 2011-01-18
Publish Date: 2011-06-22

Abstract

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.
- Non-bonded energy,
- Protocol extension,
- Discovery Studio 2.0

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References(4)

References

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