Automatic Perception of Organic Molecules Based on Essential Structural Information

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• 作者：Yuan Zhao ; Tiejun Cheng ; Renxiao Wang
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2007
• 出版时间：July 2007
• 年：2007
• 卷：47
• 期：4
• 页码：1379 - 1385
• 全文大小：116K
• 年卷期：v.47,no.4(July 2007)
• ISSN：1549-960X

文摘

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, calledI-interpret (available on-line at http://www.sioc-ccbg.ac.cn/software/I-interpret/), for interpreting the chemicalstructure of a given organic molecule merely from its essential structural information, including elementidentities and three-dimensional coordinates of its component atoms. I-interpret uses standard geometricalparameters of organic molecules in atom/bond-type assignment. A series of elaborate considerations arearranged in a logical sequence for this purpose. I-interpret was tested on a set of 179 small organic moleculesfrom 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 otherprograms under our evaluation. I-interpret also provides users some optional functions, which makes itmore flexible and powerful in practice. It may serve as a valuable tool for processing chemical structuresin molecular modeling.