Martin Stroet, Bertrand Caron, Martin S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen M. Visscher, Josef Holownia, Callum Macfarlane, Brian J. Bennion, Svetlana Gelpi-Dominguez, Felice C. Lightstone, Tijs van der Storm, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
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引用次数: 0
Abstract
An Online tool for Fragment-based Molecule Parametrization (OFraMP) is described. OFraMP is a web application for assigning atomic interaction parameters to large molecules by matching sub-fragments within the target molecule to equivalent sub-fragments within the Automated Topology Builder (ATB, atb.uq.edu.au) database. OFraMP identifies and compares alternative molecular fragments from the ATB database, which contains over 890,000 pre-parameterized molecules, using a novel hierarchical matching procedure. Atoms are considered within the context of an extended local environment (buffer region) with the degree of similarity between an atom in the target molecule and that in the proposed match controlled by varying the size of the buffer region. Adjacent matching atoms are combined into progressively larger matched sub-structures. The user then selects the most appropriate match. OFraMP also allows users to manually alter interaction parameters and automates the submission of missing substructures to the ATB in order to generate parameters for atoms in environments not represented in the existing database. The utility of OFraMP is illustrated using the anti-cancer agent paclitaxel and a dendrimer used in organic semiconductor devices.
描述了一种基于片段的分子参数化在线工具(OFraMP)。OFraMP是一个web应用程序，通过将目标分子中的子片段与自动化拓扑构建器(ATB, atb.uq.edu.au)数据库中的等效子片段进行匹配，为大分子分配原子相互作用参数。OFraMP使用一种新颖的分层匹配程序，从ATB数据库中识别和比较替代的分子片段，该数据库包含超过890,000个预参数化分子。在扩展的局部环境(缓冲区域)中考虑原子，目标分子中的原子与提议匹配中的原子之间的相似程度通过改变缓冲区域的大小来控制。相邻的匹配原子逐渐结合成更大的匹配子结构。然后用户选择最合适的匹配。OFraMP还允许用户手动更改交互参数，并自动向ATB提交缺失的子结构，以便为现有数据库中未表示的环境中的原子生成参数。利用抗癌剂紫杉醇和用于有机半导体器件的树状大分子说明了OFraMP的效用。图片摘要:应用于紫杉醇(ATB ID 35922)的framp。
期刊介绍：
The Journal of Computer-Aided Molecular Design provides a form for disseminating information on both the theory and the application of computer-based methods in the analysis and design of molecules. The scope of the journal encompasses papers which report new and original research and applications in the following areas:
- theoretical chemistry;
- computational chemistry;
- computer and molecular graphics;
- molecular modeling;
- protein engineering;
- drug design;
- expert systems;
- general structure-property relationships;
- molecular dynamics;
- chemical database development and usage.
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