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.

Graphical abstract

OFraMP applied to paclitaxel (ATB ID 35922).

中文翻译：

---

OFramp：一种基于片段的工具，有助于大分子参数化

描述了基于片段的分子参数化 (OFraMP) 的在线工具。OFraMP 是一个 Web 应用程序，用于通过将目标分子内的子片段与自动拓扑生成器（ATB、atb.uq.edu.au）数据库中的等效子片段进行匹配来为大分子分配原子相互作用参数。OFraMP 使用新颖的分层匹配程序识别并比较 ATB 数据库中的替代分子片段，该数据库包含超过 890,000 个预先参数化的分子。在扩展的局部环境（缓冲区）的背景下考虑原子，目标分子中的原子与通过改变缓冲区大小控制的拟议匹配中的原子之间的相似程度。相邻的匹配原子被组合成逐渐更大的匹配子结构。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，并自动将缺失的子结构提交给 ATB，以便为现有数据库中未表示的环境中的原子生成参数。OFraMP 的实用性通过有机半导体器件中使用的抗癌剂紫杉醇和树枝状聚合物来说明。

图形概要

OFrMP 适用于紫杉醇 (ATB ID 35922)。