ArticleJournal of computer-aided molecular design2023
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.
Article in Journal of computer-aided molecular design, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- A new method to build an initial configuration for molecular modeling.Journal of molecular modeling · 2026Article
- Structural origins of species-specific differences in TRPV2 activation.Nature communications · 2026Article
- Carbon dots and DNA: DNA binding mechanisms and their effect on the cell cycle arrest.Journal of advanced research · 2026Article
- Article
- Exploring Lamiaceae diterpenoids as potential multitarget therapeutics for leishmaniasis and chagas disease.Molecular diversity · 2026Article
- Molecular Dynamics Simulations of Plasma-Antifolate Drug Synergy in Cancer Therapy.Biomolecules · 2025Article
- Interaction of Human Respiratory Syncytial Virus (HRSV) Matrix Protein with Resveratrol Shows Antiviral Effect.International journal of molecular sciences · 2024Article
- Rational Approach toward COVID-19's Main Protease Inhibitors: A Hierarchical Biochemoinformatics Analysis.International journal of molecular sciences · 2024Article
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17 authors.
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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. OFraMP applied to paclitaxel (ATB ID 35922).
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