Shirts MR - Search Results

1

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.

2

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

Pande VS, Baker I, Chapman J, Elmer SP, Khaliq S, Larson SM, Rhee YM, Shirts MR, Snow CD, Sorin EJ, Zagrovic B. Pande VS, et al. Among authors: shirts mr. Biopolymers. 2003 Jan;68(1):91-109. doi: 10.1002/bip.10219. Biopolymers. 2003. PMID: 12579582

3

Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods.

Bu L, Beckham GT, Shirts MR, Nimlos MR, Adney WS, Himmel ME, Crowley MF. Bu L, et al. Among authors: shirts mr. J Biol Chem. 2011 May 20;286(20):18161-9. doi: 10.1074/jbc.M110.212076. Epub 2011 Mar 24. J Biol Chem. 2011. PMID: 21454590 Free PMC article.

4

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.

5

The solvation interface is a determining factor in peptide conformational preferences.

Sorin EJ, Rhee YM, Shirts MR, Pande VS. Sorin EJ, et al. Among authors: shirts mr. J Mol Biol. 2006 Feb 10;356(1):248-56. doi: 10.1016/j.jmb.2005.11.058. Epub 2005 Dec 5. J Mol Biol. 2006. PMID: 16364361

6

COMPUTING: Screen Savers of the World Unite!

Shirts M, Pande VS. Shirts M, et al. Science. 2000 Dec 8;290(5498):1903-4. doi: 10.1126/science.290.5498.1903. Science. 2000. PMID: 17742054

7

Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities.

Fuller JC, Jackson RM, Shirts MR. Fuller JC, et al. Among authors: shirts mr. J Phys Chem B. 2012 Sep 6;116(35):10856-69. doi: 10.1021/jp209041x. Epub 2012 Aug 27. J Phys Chem B. 2012. PMID: 22920218

8

Distinct aggregation mechanisms of monoclonal antibody under thermal and freeze-thaw stresses revealed by hydrogen exchange.

Zhang A, Singh SK, Shirts MR, Kumar S, Fernandez EJ. Zhang A, et al. Among authors: shirts mr. Pharm Res. 2012 Jan;29(1):236-50. doi: 10.1007/s11095-011-0538-y. Epub 2011 Jul 30. Pharm Res. 2012. PMID: 21805212

9

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E. Pronk S, et al. Among authors: shirts mr. Bioinformatics. 2013 Apr 1;29(7):845-54. doi: 10.1093/bioinformatics/btt055. Epub 2013 Feb 13. Bioinformatics. 2013. PMID: 23407358 Free PMC article.

10

Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations.

Monroe JI, El-Nahal WG, Shirts MR. Monroe JI, et al. Among authors: shirts mr. Proteins. 2014 Jan;82(1):130-44. doi: 10.1002/prot.24346. Epub 2013 Sep 17. Proteins. 2014. PMID: 23775803

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