Hayes RL - Search Results

1

Exploring pH Dependent Host/Guest Binding Affinities.

Paul TJ, Vilseck JZ, Hayes RL, Brooks CL 3rd. Paul TJ, et al. Among authors: hayes rl. J Phys Chem B. 2020 Jul 30;124(30):6520-6528. doi: 10.1021/acs.jpcb.0c03671. Epub 2020 Jul 22. J Phys Chem B. 2020. PMID: 32628482 Free PMC article.

2

Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics.

Hayes RL, Armacost KA, Vilseck JZ, Brooks CL 3rd. Hayes RL, et al. J Phys Chem B. 2017 Apr 20;121(15):3626-3635. doi: 10.1021/acs.jpcb.6b09656. Epub 2017 Feb 10. J Phys Chem B. 2017. PMID: 28112940 Free PMC article.

3

Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

Ding X, Vilseck JZ, Hayes RL, Brooks CL 3rd. Ding X, et al. Among authors: hayes rl. J Chem Theory Comput. 2017 Jun 13;13(6):2501-2510. doi: 10.1021/acs.jctc.7b00204. Epub 2017 May 26. J Chem Theory Comput. 2017. PMID: 28510433 Free PMC article.

4

CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.

Ding X, Hayes RL, Vilseck JZ, Charles MK, Brooks CL 3rd. Ding X, et al. Among authors: hayes rl. J Comput Aided Mol Des. 2018 Jan;32(1):89-102. doi: 10.1007/s10822-017-0050-5. Epub 2017 Sep 7. J Comput Aided Mol Des. 2018. PMID: 28884249 Free PMC article.

5

Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics.

Vilseck JZ, Armacost KA, Hayes RL, Goh GB, Brooks CL 3rd. Vilseck JZ, et al. Among authors: hayes rl. J Phys Chem Lett. 2018 Jun 21;9(12):3328-3332. doi: 10.1021/acs.jpclett.8b01284. Epub 2018 Jun 6. J Phys Chem Lett. 2018. PMID: 29847134 Free PMC article.

6

Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme.

Hayes RL, Vilseck JZ, Brooks CL 3rd. Hayes RL, et al. Protein Sci. 2018 Nov;27(11):1910-1922. doi: 10.1002/pro.3500. Protein Sci. 2018. PMID: 30175503 Free PMC article.

7

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing.

Widom JR, Nedialkov YA, Rai V, Hayes RL, Brooks CL 3rd, Artsimovitch I, Walter NG. Widom JR, et al. Among authors: hayes rl. Mol Cell. 2018 Nov 1;72(3):541-552.e6. doi: 10.1016/j.molcel.2018.08.046. Mol Cell. 2018. PMID: 30388413 Free PMC article.

8

Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1.

Vilseck JZ, Sohail N, Hayes RL, Brooks CL 3rd. Vilseck JZ, et al. Among authors: hayes rl. J Phys Chem Lett. 2019 Sep 5;10(17):4875-4880. doi: 10.1021/acs.jpclett.9b02004. Epub 2019 Aug 13. J Phys Chem Lett. 2019. PMID: 31386370 Free PMC article.

9

Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics.

Raman EP, Paul TJ, Hayes RL, Brooks CL 3rd. Raman EP, et al. Among authors: hayes rl. J Chem Theory Comput. 2020 Dec 8;16(12):7895-7914. doi: 10.1021/acs.jctc.0c00830. Epub 2020 Nov 17. J Chem Theory Comput. 2020. PMID: 33201701 Free PMC article.

10

A strategy for proline and glycine mutations to proteins with alchemical free energy calculations.

Hayes RL, Brooks CL 3rd. Hayes RL, et al. J Comput Chem. 2021 Jun 5;42(15):1088-1094. doi: 10.1002/jcc.26525. Epub 2021 Apr 12. J Comput Chem. 2021. PMID: 33844328 Free PMC article.

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