Advanced Automatic Generation of 3D Molecular Structures

poster · 15 years ago
by Adrián Kalászi, Gábor Imre, Ödön Farkas, Imre Jákli (ChemAxon)
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Numerous theoretical methods in the field of computational chemistry fall back on the availability of 3D structures of compounds. Determining molecular structure without human interaction is an essential component of several techniques, like QSAR, 3D pharmacophore analysis, reaction prediction, etc. Moreover, current computational tools used for structure determination, including force-fields and quantum chemical methods, require a complete set of initial 3D coordinates. The efficiency of 3D structure based HTS (high throughput screening) tools also can be enhanced by employing conformational analysis to yield multiple valid structures. Our approach utilizes a composition of several methods ranging from pure rule based1, multi dimensional distance geometry method2 to stored substructure lookup features in a flexible software framework. The actual implementation is a highly portable JAVA software, which fits in a broad scale of applications: it can be used in small web drawing applets3 as well as a standalone database processing component. The coordinate determination process is characteristically a “divide and conquer” approach: the structure is composed of fragments, which are joined together. From the available fragment conformers, the conformers of the joined structures can be generated during the fuse step. The fragment conformers are generated either through further fragmentation or with an elemental structure/conformer prediction method, consequently the conformational analysis is an inherent part of the building process (in contrast with methods proceeding from 3D initial structures4). The novelty of our approach lies in the diversity of the utilized elemental methods and the arisen scalability options. 1st European Chemistry Congress, Budapest, Hungary, 27-31 August, 2006. Download