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On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

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Mobley, David L., Chodera, John D., Dill, Ken A.·2006·The Journal of Chemical Physics

DOI 10.1063/1.2221683PMC PMC3583553

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Abstract

Alchemical free energy calculations are becoming a useful tool for calculating absolute binding free energies of small molecule ligands to proteins. Here, we find that the presence of multiple metastable ligand orientations can cause convergence problems when distance restraints alone are used. We demonstrate that the use of orientational restraints can greatly accelerate the convergence of these calculations. However, even with this acceleration, we find that sufficient sampling requires substantially longer simulations than are used in many published protocols. To further accelerate convergence, we introduce a new method of configuration space decomposition by orientation which reduces required simulation lengths by at least a factor of 5 in the cases examined. Our method is easily parallelizable, well suited for cases where a ligand cocrystal structure is not available, and can utilize initial orientations generated by docking packages.

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Authors: Mobley, D. L., Chodera, J. D., & Dill, K. A.
Affiliations: University of California, San Francisco (US)
ORCID: Mobley, David L.
Chodera, John D.
Dill, Ken A.
Venue: The Journal of Chemical Physics
Publisher: AIP Publishing
Published: 2006-08-22
Volume: 125
Issue: 8
Pages: 084902-084902
ISSN: 0021-9606 (ISSN-L)
1089-7690
DOI: 10.1063/1.2221683
PMC: PMC3583553
OpenAlex: W1965762256
Cited by: 316
References: 50
Citations by year: 2026: 6 · 2025: 14 · 2024: 19 · 2023: 18 · 2022: 23 · 2021: 18 · 2020: 18 · 2019: 13 · 2018: 17 · 2017: 15 · 2016: 13 · 2015: 11 · 2014: 17 · 2013: 16 · 2012: 20
FWCI: 12.61
Type: journal article
Language: en
Open access: green
europepmc.org
Locations: The Journal of Chemical Physics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of General Medical Sciences (R01GM063592, GM34993, R56GM063592, R01GM034993, GM 063592)
Topics: Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords: alchemical free energy calculations, absolute binding free energy, protein-ligand binding, convergence acceleration
MeSH terms: Biophysics, Catechols, Chemistry, Physical, Computer Simulation, Crystallization, Ligands, Models, Chemical, Models, Molecular, Models, Theoretical, Molecular Conformation, Proteins, Software, Thermodynamics, Models, Statistical, Phenol

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On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

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