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Michael R Shirts

TitleAssociate Professor
InstitutionUniversity of Colorado Boulder
DepartmentChemical & Biological Engin

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 Aug; 31(8):777. PMID: 28752343.
      View in: PubMed
    2. Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 Jan; 31(1):147-161. PMID: 27787702.
      View in: PubMed
    3. Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J Comput Aided Mol Des. 2016 Nov; 30(11):927-944. PMID: 27677750.
      View in: PubMed
    4. Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Overview of the SAMPL5 host-guest challenge: Are we doing better? J Comput Aided Mol Des. 2017 Jan; 31(1):1-19. PMID: 27658802.
      View in: PubMed
    5. Dybeck EC, Schieber NP, Shirts MR. Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials. J Chem Theory Comput. 2016 Aug 09; 12(8):3491-505. PMID: 27341280.
      View in: PubMed
    6. Dybeck EC, König G, Brooks BR, Shirts MR. Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials. J Chem Theory Comput. 2016 Apr 12; 12(4):1466-80. PMID: 26928941.
      View in: PubMed
    7. Naden LN, Shirts MR. Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting. J Chem Theory Comput. 2016 Apr 12; 12(4):1806-23. PMID: 26849009.
      View in: PubMed
    8. Slovin MR, Shirts MR. Identifying Differences and Similarities in Static and Dynamic Contact Angles between Nanoscale and Microscale Textured Surfaces Using Molecular Dynamics Simulations. Langmuir. 2015 Jul 28; 31(29):7980-90. PMID: 26110823.
      View in: PubMed
    9. Naden LN, Shirts MR. Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions. J Chem Theory Comput. 2015 Jun 09; 11(6):2536-49. PMID: 26575553.
      View in: PubMed
    10. Basconi JE, Carta G, Shirts MR. Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study. Langmuir. 2015 Apr 14; 31(14):4176-87. PMID: 25785668.
      View in: PubMed
    11. Klimovich PV, Shirts MR, Mobley DL. Guidelines for the analysis of free energy calculations. J Comput Aided Mol Des. 2015 May; 29(5):397-411. PMID: 25808134; PMCID: PMC4420631.
    12. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. J Chem Theory Comput. 2015 Mar 10; 11(3):1347. PMID: 26579779; PMCID: PMC4675652.
    13. Zhong ED, Shirts MR. Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations. Langmuir. 2014 May 06; 30(17):4952-61. PMID: 24716898.
      View in: PubMed
    14. Naden LN, Pham TT, Shirts MR. Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites. J Chem Theory Comput. 2014 Mar 11; 10(3):1128-49. PMID: 26580188.
      View in: PubMed
    15. Monroe JI, Shirts MR. Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations. J Comput Aided Mol Des. 2014 Apr; 28(4):401-15. PMID: 24610238.
      View in: PubMed
    16. Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT. Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy. J Am Chem Soc. 2013 Dec 18; 135(50):18831-9. PMID: 24279927.
      View in: PubMed
    17. Wang K, Chodera JD, Yang Y, Shirts MR. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J Comput Aided Mol Des. 2013 Dec; 27(12):989-1007. PMID: 24297454; PMCID: PMC4154199.
    18. Paliwal H, Shirts MR. Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions. J Chem Theory Comput. 2013 Nov 12; 9(11):4700-17. PMID: 26583389.
      View in: PubMed
    19. Monroe JI, El-Nahal WG, Shirts MR. Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations. Proteins. 2014 Jan; 82(1):130-44. PMID: 23775803.
      View in: PubMed
    20. Basconi JE, Shirts MR. Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations. J Chem Theory Comput. 2013 Jul 09; 9(7):2887-99. PMID: 26583973.
      View in: PubMed
    21. Paliwal H, Shirts MR. Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude. J Chem Phys. 2013 Apr 21; 138(15):154108. PMID: 23614413.
      View in: PubMed
    22. 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. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013 Apr 01; 29(7):845-54. PMID: 23407358; PMCID: PMC3605599.
    23. Shirts MR. Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles. J Chem Theory Comput. 2013 Feb 12; 9(2):909-26. PMID: 26588735.
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    24. Shirts MR, Mobley DL. An introduction to best practices in free energy calculations. Methods Mol Biol. 2013; 924:271-311. PMID: 23034753.
      View in: PubMed
    25. Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, Pande VS. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. J Chem Theory Comput. 2013 Jan 08; 9(1):461-469. PMID: 23316124.
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    26. Fuller JC, Jackson RM, Shirts MR. Configurational preferences of arylamide a-helix mimetics via alchemical free energy calculations of relative binding affinities. J Phys Chem B. 2012 Sep 06; 116(35):10856-69. PMID: 22920218.
      View in: PubMed
    27. Fuller JC, Jackson RM, Edwards TA, Wilson AJ, Shirts MR. Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable. PLoS One. 2012; 7(8):e43253. PMID: 22916232; PMCID: PMC3423354.
    28. Bu L, Nimlos MR, Shirts MR, Ståhlberg J, Himmel ME, Crowley MF, Beckham GT. Product binding varies dramatically between processive and nonprocessive cellulase enzymes. J Biol Chem. 2012 Jul 13; 287(29):24807-13. PMID: 22648408; PMCID: PMC3397907.
    29. Pham TT, Shirts MR. Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase. J Chem Phys. 2012 Mar 28; 136(12):124120. PMID: 22462848.
      View in: PubMed
    30. Shirts MR. Best practices in free energy calculations for drug design. Methods Mol Biol. 2012; 819:425-67. PMID: 22183551.
      View in: PubMed
    31. Chodera JD, Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. J Chem Phys. 2011 Nov 21; 135(19):194110. PMID: 22112069.
      View in: PubMed
    32. Paliwal H, Shirts MR. A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods. J Chem Theory Comput. 2011 Dec 13; 7(12):4115-34. PMID: 26598357.
      View in: PubMed
    33. Zhang A, Singh SK, Shirts MR, Kumar S, Fernandez EJ. Distinct aggregation mechanisms of monoclonal antibody under thermal and freeze-thaw stresses revealed by hydrogen exchange. Pharm Res. 2012 Jan; 29(1):236-50. PMID: 21805212.
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    34. Pham TT, Shirts MR. Identifying low variance pathways for free energy calculations of molecular transformations in solution phase. J Chem Phys. 2011 Jul 21; 135(3):034114. PMID: 21786994.
      View in: PubMed
    35. Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS. Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. J Chem Phys. 2011 Jun 28; 134(24):244107. PMID: 21721612; PMCID: PMC3143679.
    36. Bu L, Beckham GT, Shirts MR, Nimlos MR, Adney WS, Himmel ME, Crowley MF. Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods. J Biol Chem. 2011 May 20; 286(20):18161-9. PMID: 21454590; PMCID: PMC3093888.
    37. Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol. 2011 Apr; 21(2):150-60. PMID: 21349700; PMCID: PMC3085996.
    38. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. J Chem Theory Comput. 2009 Feb 10; 5(2):350-358. PMID: 20150953.
      View in: PubMed
    39. Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys. 2008 Sep 28; 129(12):124105. PMID: 19045004; PMCID: PMC2671659.
    40. Zhu K, Shirts MR, Friesner RA. Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program:? Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects. J Chem Theory Comput. 2007 Nov; 3(6):2108-19. PMID: 26636204.
      View in: PubMed
    41. Shirts MR, Mobley DL, Chodera JD, Pande VS. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. J Phys Chem B. 2007 Nov 15; 111(45):13052-63. PMID: 17949030.
      View in: PubMed
    42. Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. J Chem Theory Comput. 2007 Mar; 3(2):640-8. PMID: 26637042.
      View in: PubMed
    43. Jayachandran G, Shirts MR, Park S, Pande VS. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J Chem Phys. 2006 Aug 28; 125(8):084901. PMID: 16965051.
      View in: PubMed
    44. Sorin EJ, Rhee YM, Shirts MR, Pande VS. The solvation interface is a determining factor in peptide conformational preferences. J Mol Biol. 2006 Feb 10; 356(1):248-56. PMID: 16364361.
      View in: PubMed
    45. Fujitani H, Tanida Y, Ito M, Jayachandran G, Snow CD, Shirts MR, Sorin EJ, Pande VS. Direct calculation of the binding free energies of FKBP ligands. J Chem Phys. 2005 Aug 22; 123(8):084108. PMID: 16164283.
      View in: PubMed
    46. Shirts MR, Pande VS. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. J Chem Phys. 2005 Apr 08; 122(14):144107. PMID: 15847516.
      View in: PubMed
    47. Shirts MR, Pande VS. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. J Chem Phys. 2005 Apr 01; 122(13):134508. PMID: 15847482.
      View in: PubMed
    48. Shirts MR, Bair E, Hooker G, Pande VS. Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. Phys Rev Lett. 2003 Oct 03; 91(14):140601. PMID: 14611511.
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    49. Pande VS, Baker I, Chapman J, Elmer SP, Khaliq S, Larson SM, Rhee YM, Shirts MR, Snow CD, Sorin EJ, Zagrovic B. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers. 2003 Jan; 68(1):91-109. PMID: 12579582.
      View in: PubMed
    50. Zagrovic B, Snow CD, Shirts MR, Pande VS. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol. 2002 Nov 08; 323(5):927-37. PMID: 12417204.
      View in: PubMed
    51. Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS. Native-like mean structure in the unfolded ensemble of small proteins. J Mol Biol. 2002 Oct 11; 323(1):153-64. PMID: 12368107.
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    52. Shirts MR, Pande VS. Mathematical analysis of coupled parallel simulations. Phys Rev Lett. 2001 May 28; 86(22):4983-7. PMID: 11384401.
      View in: PubMed
    53. Shirts M, Pande VS. COMPUTING: Screen Savers of the World Unite! Science. 2000 Dec 08; 290(5498):1903-4. PMID: 17742054.
      View in: PubMed
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