OFraMP: a fragment-based tool to facilitate the parametrization of large molecules

Stroet, Martin; Caron, Bertrand; Engler, Martin S.; van der Woning, Jimi; Kauffmann, Aude; van Dijk, Marc; El-Kebir, Mohammed; Visscher, Koen M.; Holownia, Josef; Macfarlane, Callum; Bennion, Brian J.; Gelpi-Dominguez, Svetlana; Lightstone, Felice C.; van der Storm, Tijs; Geerke, Daan P.; Mark, Alan E.; Klau, Gunnar W.

doi:10.1007/s10822-023-00511-7

Title: OFraMP: a fragment-based tool to facilitate the parametrization of large molecules

Journal Article · 13 June 2023 · Journal of Computer-Aided Molecular Design

DOI: https://doi.org/10.1007/s10822-023-00511-7 · OSTI ID:1984881

; Caron, Bertrand;

; van der Woning, Jimi;

;

; Visscher, Koen M.;

;

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. Graphical abstract OFraMP applied to paclitaxel (ATB ID 35922).

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Sponsoring Organization:: USDOE

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1984881

Journal Information:: Journal of Computer-Aided Molecular Design, Journal Name: Journal of Computer-Aided Molecular Design Journal Issue: 8 Vol. 37; ISSN 0920-654X

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: Netherlands

Language:: English

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