title: [An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level].
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.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.
authors.forename: Yue-Dong
authors.initials: YD
authors.lastname: Gao
authors.forename: Jing-Fei
authors.initials: JF
authors.lastname: Huang
mesh_terms: D055598:Chemical Phenomena; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D004247:DNA / Q000737:chemistry; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA