Shirts MR - Search Results

1

Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation.

Hsu WT, Ramirez DA, Sammakia T, Tan Z, Shirts MR. Hsu WT, et al. Among authors: shirts mr. J Comput Aided Mol Des. 2022 Apr;36(4):313-328. doi: 10.1007/s10822-022-00453-6. Epub 2022 May 4. J Comput Aided Mol Des. 2022. PMID: 35507105 Free PMC article.

2

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.

Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang LP, Cole DJ, Gilson MK, Chodera JD, Bayly CI, Shirts MR, Mobley DL. Boothroyd S, et al. Among authors: shirts mr. J Chem Theory Comput. 2023 Jun 13;19(11):3251-3275. doi: 10.1021/acs.jctc.3c00039. Epub 2023 May 11. J Chem Theory Comput. 2023. PMID: 37167319 Free PMC article.

3

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.

Wang K, Chodera JD, Yang Y, Shirts MR. Wang K, et al. Among authors: shirts mr. J Comput Aided Mol Des. 2013 Dec;27(12):989-1007. doi: 10.1007/s10822-013-9689-8. Epub 2013 Dec 3. J Comput Aided Mol Des. 2013. PMID: 24297454 Free PMC article.

4

Overview of the SAMPL5 host-guest challenge: Are we doing better?

Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Yin J, et al. Among authors: shirts mr. J Comput Aided Mol Des. 2017 Jan;31(1):1-19. doi: 10.1007/s10822-016-9974-4. Epub 2016 Sep 22. J Comput Aided Mol Des. 2017. PMID: 27658802 Free PMC article. Review.

5

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Bannan CC, et al. Among authors: shirts mr. J Comput Aided Mol Des. 2016 Nov;30(11):927-944. doi: 10.1007/s10822-016-9954-8. Epub 2016 Sep 27. J Comput Aided Mol Des. 2016. PMID: 27677750 Free PMC article.

6

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Shirts MR, et al. J Comput Aided Mol Des. 2017 Jan;31(1):147-161. doi: 10.1007/s10822-016-9977-1. Epub 2016 Oct 27. J Comput Aided Mol Des. 2017. PMID: 27787702 Free PMC article.

7

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Shirts MR, et al. J Comput Aided Mol Des. 2017 Aug;31(8):777. doi: 10.1007/s10822-017-0043-4. J Comput Aided Mol Des. 2017. PMID: 28752343 No abstract available.

8

Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations.

Hsu WT, Piomponi V, Merz PT, Bussi G, Shirts MR. Hsu WT, et al. Among authors: shirts mr. J Chem Theory Comput. 2023 Mar 28;19(6):1805-1817. doi: 10.1021/acs.jctc.2c01258. Epub 2023 Feb 28. J Chem Theory Comput. 2023. PMID: 36853624

9

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations.

Monroe JI, Shirts MR. Monroe JI, et al. Among authors: shirts mr. J Comput Aided Mol Des. 2014 Apr;28(4):401-15. doi: 10.1007/s10822-014-9716-4. Epub 2014 Mar 8. J Comput Aided Mol Des. 2014. PMID: 24610238

10

Guidelines for the analysis of free energy calculations.

Klimovich PV, Shirts MR, Mobley DL. Klimovich PV, et al. Among authors: shirts mr. J Comput Aided Mol Des. 2015 May;29(5):397-411. doi: 10.1007/s10822-015-9840-9. Epub 2015 Mar 26. J Comput Aided Mol Des. 2015. PMID: 25808134 Free PMC article.

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