title: Automatic perception of organic molecules based on essential structural information.
abstract: Format conversion is very common in structure preparation in molecular modeling studies. Unfortunately, format conversion cannot always be executed precisely. We have developed an automatic method, called I-interpret (available on-line at http://www.sioc-ccbg.ac.cn/software/I-interpret/), for interpreting the chemical structure of a given organic molecule merely from its essential structural information, including element identities and three-dimensional coordinates of its component atoms. I-interpret uses standard geometrical parameters of organic molecules in atom/bond-type assignment. A series of elaborate considerations are arranged in a logical sequence for this purpose. I-interpret was tested on a set of 179 small organic molecules from the Protein Data Bank and a set of 1990 organic molecules from the NCI diversity set. On both sets, it achieved a success rate of over 95% in interpreting the correct chemical structures, outperforming other programs under our evaluation. I-interpret also provides users some optional functions, which makes it more flexible and powerful in practice. It may serve as a valuable tool for processing chemical structures in molecular modeling.
authors.affiliation: State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai 200032, People's Republic of China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Tiejun
authors.initials: T
authors.lastname: Cheng
authors.forename: Renxiao
authors.initials: R
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D001331:Automation; D008670:Metals / Q000737:chemistry; D015394:Molecular Structure; D009930:Organic Chemicals / Q000737:chemistry*
chemical_list: D008670:Metals; D009930:Organic Chemicals