ArticleJournal of computational chemistry2015
Parametrization of macrolide antibiotics using the force field toolkit.
Article in Journal of computational chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed, 22 citations in OpenAlex.
- Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly.Journal of chemical information and modeling · 2025Article
- Broadening access to small-molecule parameterization with the force field toolkit.The Journal of chemical physics · 2024Article
- Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials.EMBO reports · 2023Review
- On the force field optimisation ofJournal of computer-aided molecular design · 2022Article
- The Mechanism of Action of Hepatitis B Virus Capsid Assembly Modulators Can Be Predicted from Binding to Early Assembly Intermediates.Journal of medicinal chemistry · 2022Article
- CHARMM force field generation for a cationic thiophene oligomer with ffTK.Journal of molecular modeling · 2021Article
- Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison.The Journal of chemical physics · 2020Article
- Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics.International journal of molecular sciences · 2020Review
- Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.Journal of chemical theory and computation · 2018Article
- The macrolide antibiotic renaissance.British journal of pharmacology · 2017Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. Here, we determine CHARMM-compatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (ffTK) plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.