Please wait a minute...
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
Download: PDF(246 KB)  
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks    
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  
Corresponding Authors: HUANG Jing-Fei   
About author: GAO Yue-Dong
Issue Date: 22 June 2011
E-mail this article
E-mail Alert
Articles by authors
Cite this article:   
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.
URL:     OR
Ashenhurst JA. 2010. Intermolecular oxidative cross-coupling of arenes [J]. Chem Soc Rev, 39(2): 540-548.
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations [J]. J Comut Chem, 4: 187-217.
Hirashima A, Huang H. 2008. Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana [J]. Comput Biol Chem, 32(3): 185-190.
McCullagh M, Prytkova T, Tonzani S, Winter ND, Schatz GC. 2008. Modeling self-assembly processes driven by nonbonded interactions in soft materials [J]. J Phys Chem B, 112(34): 10388-10398.
Nakashima H, Furukawa K, Kashimura Y, Torimitsu K. 2008. Self-assembly of gold nanorods induced by intermolecular interactions of surface- anchored lipids
[J]. Langmuir, 24(11): 5654-5658.
Pyrkov TV, Ozerov IV, Blitskaia ED, Efremov RG. 2010. Molecular docking: role of intermolecular contacts in formation of complexes of proteins with nucleotides and peptides
[J]. Bioorg Khim, 36(4): 482-492.
Sagui C, Darden TA. 1999. Molecular dynamics simulations of biomolecules: long-range electrostatic effects [J]. Annu Rev Biophys Biomol Struct, 28: 155-179.
Shuman S, Lima CD. 2004. The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases [J]. Curr Opin Struct Biol, 14(6): 757-764.
Spassov VZ, Yan L. 2008. A fast and accurate computational approach to protein ionization [J]. Protein Sci, 17(11): 1955-1970.
Spriggs S, Garyu L, Connor R, Summers MF. 2008. Potential intra- and intermolecular interactions involving the unique-5' region of the HIV-1 5'-UTR [J]. Biochemistry, 47(49): 13064-13073.
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. 2002. The Bioperl toolkit: Perl modules for the life sciences [J]. Genome Res, 12(10): 1611-1618.
Sundaram K, Prasad CV. 1982. A program to calculate non-bonded interaction energy in biomolecular aggregates [J]. Comput Programs Biomed, 14(1): 41-46.
Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. 2005. GROMACS: fast, flexible, and free [J]. J Comput Chem, 26(16): 1701-1718.
Wang LK, Nair PA, Shuman S. 2008. Structure-guided mutational analysis of the OB, HhH, and BRCT domains of Escherichia coli DNA ligase [J]. J Biol Chem, 283(34): 23343-23352.
Wang LK, Zhu H, Shuman S. 2009. Structure-guided mutational analysis of the nucleotidyltransferase domain of escherichia coli DNA ligase (LigA) [J]. J Biol Chem, 284(13): 8486-8494.
Waters ML. 2002. Aromatic interactions in model systems [J]. Curr Opin Chem Biol, 6(6): 736-741.
Weiner PK, Kollman PA. 1981. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions [J]. J Comput Chem, 2: 287-303.

[1] SHENG Zi-Zhang,HUANG Jing-Fei. Functional site prediction of BRCT domain containing phosphate binding pocket[J]. ZOOLOGICAL RESEARCH, 2011, 32(5): 509-514.
Full text