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Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host-guest SAMPL9 blinded challenge.
Phys Chem Chem Phys. 2023 Sep 20;25(36):24364-24376. doi: 10.1039/d3cp02125d.
Phys Chem Chem Phys. 2023.
PMID: 37676233
Alchemical transformations for concerted hydration free energy estimation with explicit solvation.
Khuttan S, Azimi S, Wu JZ, Gallicchio E.
Khuttan S, et al.
J Chem Phys. 2021 Feb 7;154(5):054103. doi: 10.1063/5.0036944.
J Chem Phys. 2021.
PMID: 33557533
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Alchemical Transfer Approach to Absolute Binding Free Energy Estimation.
Wu JZ, Azimi S, Khuttan S, Deng N, Gallicchio E.
Wu JZ, et al. Among authors: khuttan s.
J Chem Theory Comput. 2021 Jun 8;17(6):3309-3319. doi: 10.1021/acs.jctc.1c00266. Epub 2021 May 13.
J Chem Theory Comput. 2021.
PMID: 33983730
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Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method.
Azimi S, Khuttan S, Wu JZ, Pal RK, Gallicchio E.
Azimi S, et al. Among authors: khuttan s.
J Chem Inf Model. 2022 Jan 24;62(2):309-323. doi: 10.1021/acs.jcim.1c01129. Epub 2022 Jan 6.
J Chem Inf Model. 2022.
PMID: 34990555
Free article.
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Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge.
Azimi S, Wu JZ, Khuttan S, Kurtzman T, Deng N, Gallicchio E.
Azimi S, et al. Among authors: khuttan s.
J Comput Aided Mol Des. 2022 Jan;36(1):63-76. doi: 10.1007/s10822-021-00437-y. Epub 2022 Jan 21.
J Comput Aided Mol Des. 2022.
PMID: 35059940
Free PMC article.
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What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling.
Khuttan S, Gallicchio E.
Khuttan S, et al.
J Chem Theory Comput. 2024 Feb 13;20(3):1489-1501. doi: 10.1021/acs.jctc.3c01250. Epub 2024 Jan 22.
J Chem Theory Comput. 2024.
PMID: 38252868
Free PMC article.
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