Cited by 237Computational Drug Discovery MethodsAdvanced Chemical Physics StudiesProtein Structure and Dynamics

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Using AMBER18 for Relative Free Energy Calculations

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Song, Lin Frank, Lee, Tai-Sung, Zhu, Chun, York, Darrin M., Merz, Kenneth M.·2019·Journal of Chemical Information and Modeling

DOI 10.1021/acs.jcim.9b00105PMC PMC7371000

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Abstract

With renewed interest in free energy methods in contemporary structure-based drug design, there is a pressing need to validate against multiple targets and force fields to assess the overall ability of these methods to accurately predict relative binding free energies. We computed relative binding free energies using graphics processing unit accelerated thermodynamic integration (GPU-TI) on a data set originally assembled by Schrödinger, Inc. Using their GPU free energy code (FEP+) and the OPLS2.1 force field combined with the REST2 enhanced sampling approach, these authors obtained an overall MUE of 0.9 kcal/mol and an overall RMSD of 1.14 kcal/mol. In our study using GPU-TI from AMBER with the AMBER14SB/GAFF1.8 force field but without enhanced sampling, we obtained an overall MUE of 1.17 kcal/mol and an overall RMSD of 1.50 kcal/mol for the 330 perturbations contained in this data set. A more detailed analysis of our results suggested that the observed differences between the two studies arise from differences in sampling protocols along with differences in the force fields employed. Future work should address the problem of establishing benchmark quality results with robust statistical error bars obtained through multiple independent runs and enhanced sampling, which is possible with the GPU-accelerated features in AMBER.

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Authors: Song, L. F., Lee, T.-S., Zhu, C., York, D. M., & Merz, K. M.
Affiliations: Michigan State University (US)
Rutgers, The State University of New Jersey (US)
Corresponding author: Merz, Kenneth M.
ORCID: Song, Lin Frank
Lee, Tai-Sung
Zhu, Chun
York, Darrin M.
Merz, Kenneth M.
Venue: Journal of Chemical Information and Modeling
Publisher: American Chemical Society (ACS)
Published: 2019-06-06
Volume: 59
Issue: 7
Pages: 3128-3135
ISSN: 1549-9596 (ISSN-L)
1549-960X
DOI: 10.1021/acs.jcim.9b00105
PMC: PMC7371000
OpenAlex: W2949467224
Cited by: 234
References: 62
Citations by year: 2026: 20 · 2025: 32 · 2024: 37 · 2023: 35 · 2022: 45 · 2021: 30 · 2020: 31 · 2019: 4
FWCI: 18.88
Type: journal article
Language: en
Open access: green
doi.org
Licence: cc-by
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-045 (stm-asf)
Locations: Journal of Chemical Information and Modeling (publishedVersion)
ChemRxiv (acceptedVersion, cc-by)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Royal College of Surgeons in Ireland (submittedVersion, cc-by)
Funders: Efficacy and Mechanism Evaluation Programme (GM107485)
Topics: Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords: relative binding free energy, thermodynamic integration, GPU acceleration, structure-based drug design, benchmarking, enhanced sampling, REST2, free energy perturbation, ligand binding prediction
MeSH terms: Computer Graphics, Models, Molecular, Protein Binding, Software, Thermodynamics, Drug Design, Molecular Structure, Molecular Dynamics Simulation

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Using AMBER18 for Relative Free Energy Calculations

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