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Michael R Shirts

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentChemical & Biological Engin

    Collapse Research 
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    R01GM132386     (SHIRTS, MICHAEL R)Mar 1, 2020 - Feb 28, 2025
    NIH
    Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug design
    Role: Principal Investigator
    R01GM115790     (KASSON, PETER M)May 1, 2016 - Apr 30, 2021
    NIH
    Hardening and Development of the GROMACS Molecular Simulation Engine
    Role: Co-Principal Investigator
    F32GM074384     (SHIRTS, MICHAEL R)May 1, 2005 - Apr 30, 2008
    NIH
    Drug Binding Free Energies with Implicit Solvent Methods
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    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. Ram?ak M, Ramirez DA, Hough LE, Shirts MR, Vidmar S, Eler?ic Filipic K, Anderluh G, Jerala R. Programmable de novo designed coiled coil-mediated phase separation in mammalian cells. Nat Commun. 2023 Dec 02; 14(1):7973. PMID: 38042897.
      View in: PubMed
    2. Friedman AJ, Padgette HM, Kramer L, Liechty ET, Donovan GW, Fox JM, Shirts MR. Biophysical Rationale for the Selective Inhibition of PTP1B over TCPTP by Nonpolar Terpenoids. J Phys Chem B. 2023 10 05; 127(39):8305-8316. PMID: 37729547.
      View in: PubMed
    3. Liechty ET, Hren A, Kramer L, Donovan G, Friedman AJ, Shirts MR, Fox JM. Analysis of neutral mutational drift in an allosteric enzyme. Protein Sci. 2023 08; 32(8):e4719. PMID: 37402140.
      View in: PubMed
    4. Ramirez DA, Hough LE, Shirts MR. Coiled-coil domains are sufficient to drive liquid-liquid phase separation of proteins in molecular models. bioRxiv. 2023 Jul 24. PMID: 37398035.
      View in: PubMed
    5. 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. Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. J Chem Theory Comput. 2023 Jun 13; 19(11):3251-3275. PMID: 37167319.
      View in: PubMed
    6. Madin OC, Shirts MR. Using physical property surrogate models to perform accelerated multi-fidelity optimization of force field parameters. Digit Discov. 2023 Jun 12; 2(3):828-847. PMID: 37312680.
      View in: PubMed
    7. Friedman AJ, Padgette HM, Kramer L, Liechty ET, Donovan GW, Fox JM, Shirts MR. A biophysical rationale for the selective inhibition of PTP1B over TCPTP by nonpolar terpenoids. bioRxiv. 2023 Apr 18. PMID: 37131728.
      View in: PubMed
    8. Hsu WT, Piomponi V, Merz PT, Bussi G, Shirts MR. Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. J Chem Theory Comput. 2023 Mar 28; 19(6):1805-1817. PMID: 36853624.
      View in: PubMed
    9. Sahu S, Schwindt NS, Coscia BJ, Shirts MR. Obtaining and Characterizing Stable Bicontinuous Cubic Morphologies and Their Nanochannels in Lyotropic Liquid Crystal Membranes. J Phys Chem B. 2022 12 08; 126(48):10098-10110. PMID: 36417348.
      View in: PubMed
    10. Friedman AJ, Liechty ET, Kramer L, Sarkar A, Fox JM, Shirts MR. Allosteric Inhibition of PTP1B by a Nonpolar Terpenoid. J Phys Chem B. 2022 10 27; 126(42):8427-8438. PMID: 36223525.
      View in: PubMed
    11. Fobe TL, Walker CC, Meek GA, Shirts MR. Folding Coarse-Grained Oligomer Models with PyRosetta. J Chem Theory Comput. 2022 Oct 11; 18(10):6354-6369. PMID: 36179376.
      View in: PubMed
    12. Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. J Chem Theory Comput. 2022 Jun 14; 18(6):3577-3592. PMID: 35533269.
      View in: PubMed
    13. Hsu WT, Ramirez DA, Sammakia T, Tan Z, Shirts MR. Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation. J Comput Aided Mol Des. 2022 04; 36(4):313-328. PMID: 35507105.
      View in: PubMed
    14. Boothroyd S, Wang LP, Mobley DL, Chodera JD, Shirts MR. Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. J Chem Theory Comput. 2022 Jun 14; 18(6):3566-3576. PMID: 35507313.
      View in: PubMed
    15. Madin OC, Boothroyd S, Messerly RA, Fass J, Chodera JD, Shirts MR. Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. J Chem Inf Model. 2022 02 28; 62(4):874-889. PMID: 35129974.
      View in: PubMed
    16. Merz PT, Hsu WT, Thompson MW, Boothroyd S, Walker CC, Shirts MR. physical_validation: A Python package to assess the physical validity of molecular simulation results. J Open Source Softw. 2022; 7(69). PMID: 36337282.
      View in: PubMed
    17. Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, Gilson MK, Chodera JD, Bayly CI, Mobley DL, Wang LP. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. J Chem Theory Comput. 2021 Oct 12; 17(10):6262-6280. PMID: 34551262.
      View in: PubMed
    18. Zhang S, Hahn DF, Shirts MR, Voelz VA. Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies. J Chem Theory Comput. 2021 Oct 12; 17(10):6536-6547. PMID: 34516130.
      View in: PubMed
    19. Walker CC, Meek GA, Fobe TL, Shirts MR. Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure. J Chem Theory Comput. 2021 Oct 12; 17(10):6018-6035. PMID: 34495659.
      View in: PubMed
    20. Kleman AF, Dufek DL, Fobe TL, McCaslin DR, Cary BP, Shirts MR, Gellman SH. Potential Foldamers Based on an ortho-Terphenyl Amino Acid. Org Lett. 2021 06 18; 23(12):4855-4859. PMID: 34077213.
      View in: PubMed
    21. Abraham NS, Shirts MR. Statistical Mechanical Approximations to More Efficiently Determine Polymorph Free Energy Differences for Small Organic Molecules. J Chem Theory Comput. 2020 Oct 13; 16(10):6503-6512. PMID: 32877183.
      View in: PubMed
    22. Coscia BJ, Calderon CP, Shirts MR. Statistical Inference of Transport Mechanisms and Long Time Scale Behavior from Time Series of Solute Trajectories in Nanostructured Membranes. J Phys Chem B. 2020 09 17; 124(37):8110-8123. PMID: 32790365.
      View in: PubMed
    23. Coscia BJ, Shirts MR. Capturing Subdiffusive Solute Dynamics and Predicting Selectivity in Nanoscale Pores with Time Series Modeling. J Chem Theory Comput. 2020 Sep 08; 16(9):5456-5473. PMID: 32786916.
      View in: PubMed
    24. Shirts MR, Ferguson AL. Statistically Optimal Continuous Free Energy Surfaces from Biased Simulations and Multistate Reweighting. J Chem Theory Comput. 2020 Jul 14; 16(7):4107-4125. PMID: 32497425.
      View in: PubMed
    25. Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, Mobley DL, Chodera JD. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J Comput Aided Mol Des. 2020 05; 34(5):601-633. PMID: 31984465.
      View in: PubMed
    26. Mey ASJS, Allen BK, Macdonald HEB, Chodera JD, Hahn DF, Kuhn M, Michel J, Mobley DL, Naden LN, Prasad S, Rizzi A, Scheen J, Shirts MR, Tresadern G, Xu H. Best Practices for Alchemical Free Energy Calculations [Article v1.0]. Living J Comput Mol Sci. 2020; 2(1). PMID: 34458687.
      View in: PubMed
    27. Coscia BJ, Shirts MR. Chemically Selective Transport in a Cross-Linked HII Phase Lyotropic Liquid Crystal Membrane. J Phys Chem B. 2019 07 25; 123(29):6314-6330. PMID: 31247136.
      View in: PubMed
    28. Schieber NP, Shirts MR. Configurational mapping significantly increases the efficiency of solid-solid phase coexistence calculations via molecular dynamics: Determining the FCC-HCP coexistence line of Lennard-Jones particles. J Chem Phys. 2019 Apr 28; 150(16):164112. PMID: 31042900.
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    29. Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward Learned Chemical Perception of Force Field Typing Rules. J Chem Theory Comput. 2019 Jan 08; 15(1):402-423. PMID: 30512951.
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    30. Coscia BJ, Yelk J, Glaser MA, Gin DL, Feng X, Shirts MR. Understanding the Nanoscale Structure of Inverted Hexagonal Phase Lyotropic Liquid Crystal Polymer Membranes. J Phys Chem B. 2019 01 10; 123(1):289-309. PMID: 30521339.
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    31. Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. Escaping Atom Types in Force Fields Using Direct Chemical Perception. J Chem Theory Comput. 2018 Nov 13; 14(11):6076-6092. PMID: 30351006.
      View in: PubMed
    32. Abraham NS, Shirts MR. Thermal Gradient Approach for the Quasi-harmonic Approximation and Its Application to Improved Treatment of Anisotropic Expansion. J Chem Theory Comput. 2018 Nov 13; 14(11):5904-5919. PMID: 30281302.
      View in: PubMed
    33. Messerly RA, Shirts MR, Kazakov AF. Uncertainty quantification confirms unreliable extrapolation toward high pressures for united-atom Mie ?-6 force field. J Chem Phys. 2018 Sep 21; 149(11):114109. PMID: 30243285.
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    34. Merz PT, Shirts MR. Testing for physical validity in molecular simulations. PLoS One. 2018; 13(9):e0202764. PMID: 30188933.
      View in: PubMed
    35. Messerly RA, Razavi SM, Shirts MR. Configuration-Sampling-Based Surrogate Models for Rapid Parameterization of Non-Bonded Interactions. J Chem Theory Comput. 2018 Jun 12; 14(6):3144-3162. PMID: 29727563.
      View in: PubMed
    36. Schieber NP, Dybeck EC, Shirts MR. Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams. J Chem Phys. 2018 Apr 14; 148(14):144104. PMID: 29655343.
      View in: PubMed
    37. 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 08; 31(8):777. PMID: 28752343.
      View in: PubMed
    38. Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. J Chem Eng Data. 2017 May 11; 62(5):1559-1569. PMID: 29056756.
      View in: PubMed
    39. 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 01; 31(1):147-161. PMID: 27787702.
      View in: PubMed
    40. 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 11; 30(11):927-944. PMID: 27677750.
      View in: PubMed
    41. 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 01; 31(1):1-19. PMID: 27658802.
      View in: PubMed
    42. 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
    43. Dybeck EC, K?nig 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
    44. 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
    45. 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
    46. 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
    47. 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.
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    48. 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.
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    49. 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.
      View in: PubMed
    50. 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
    51. 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
    52. 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.
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    53. 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.
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    54. 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.
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    55. 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
    56. 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.
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    57. 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.
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    58. 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.
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    59. Pronk S, P?ll 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.
      View in: PubMed
    60. 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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    61. Shirts MR, Mobley DL. An introduction to best practices in free energy calculations. Methods Mol Biol. 2013; 924:271-311. PMID: 23034753.
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    62. 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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    63. 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.
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    64. 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.
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    65. Bu L, Nimlos MR, Shirts MR, St?hlberg 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.
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    66. 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.
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    67. Shirts MR. Best practices in free energy calculations for drug design. Methods Mol Biol. 2012; 819:425-67. PMID: 22183551.
      View in: PubMed
    68. 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.
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    69. 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.
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    70. 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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    71. 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.
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    72. Chodera JD, Swope WC, No? 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.
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    73. 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.
      View in: PubMed
    74. 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.
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    75. 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.
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    76. Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys. 2008 Sep 28; 129(12):124105. PMID: 19045004.
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    77. 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.
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    78. 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.
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    79. 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.
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    80. 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.
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    81. 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.
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    82. 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.
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    83. 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.
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    84. 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.
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    85. 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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    86. 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.
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    87. Shirts M, Pande VS. COMPUTING: Screen Savers of the World Unite! Science. 2000 Dec 08; 290(5498):1903-4. PMID: 17742054.
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