Publications
  1. H. Paliwal and M. R. Shirts, Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude. Journal of Chemical Physics, 138(15), 154108 (2013) doi

  2. S. Pronk, S. Pali, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, E. Lindahl, GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845-854 (2013) doi

  3. M. R. Shirts, Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles. Journal of Chemical Theory and Computation, 9(2), 909-926 (2013) doi Accompanying code

  4. M R. Shirts and D. L. Mobley, "An Introduction to Best Practices in Free Energy Calculations" in Biomolecular Simulations: Methods and Protocols, Eds. L. Monticelli and E. Salonen, New York: Humana Press (2013) doi

  5. P. K. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, and V. S. Pande. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. Journal of Chemical Theory and Computation, 9(1), 461-469 (2013) doi

  6. J. C. Fuller, R. M. Jackson and M. R. Shirts, Configurational preferences of arylamide N1-helix mimetics via alchemical free energy calculations of relative binding affinities. Journal of Physical Chemistry B, 116(35), 10856-10869 (2012) doi

  7. J. C. Fuller, R. M. Jackson, A. Wilson, T. Edwards and M. R. Shirts, Modeling of Arylamide Helix Mimetics in the p53 Peptide Binding Site of hDM2 Suggests Parallel and Anti-Parallel Conformations Are Both Stable. PLoS ONE 7(8), e43253 (2012) doi

  8. L. Bu, M .R. Nimlos, M. R. Shirts, J. Stahlberg, M. E. Himmel, M. F. Crowley, G. F. Beckham, Product binding varies dramatically between processive and nonprocessive cellulase enzymes. Journal of Biological Chemistry, 287(29), 24807-24813 (2012) doi

  9. T. T. Pham and M. R. Shirts. Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase. Journal of Chemical Physics, 136, 124120 (2012) doi

  10. A. Zhang, S. K. Singh, M. R. Shirts, S. Kumar, and E. J. Fernandez. Distinct aggregation mechanisms of monoclonal antibody under thermal and freeze-thaw stresses revealed by hydrogen exchange. Pharmaceutical Research 29, 236-250 (2012) doi

  11. J. D. Chodera and M. R. Shirts. Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing. Journal of Chemical Physics, 135, 194110 (2011) doi

  12. H. Paliwal and M. R. Shirts. A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods. Journal of Chemical Theory and Computation, 7, 4115-4134 (2011) doi

  13. T. T. Pham and M. R. Shirts. Identifying Low Variance Pathways for Free Energy Calculations of Molecular Transformations in Solution Phase. Journal of Chemical Physics, 135, 034114 (2011) doi

  14. J. D. Chodera, W. C. Swope, F. Noe, J.-H. Prinz, M. R. Shirts, and V. S. Pande. Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures. Journal of Chemical Physics, 134, 244107 (2011) doi

  15. J. D. Chodera, D. L. Mobley, M. R Shirts, R. W. Dixon, K. Branson and V. S. Pande. Alchemical free energy methods for drug discovery: progress and challenges. Current Opinion in Structural Biology, 21, 150-160 (2011) doi

  16. L. Bu, G. T. Beckham, M. R. Shirts, M. R. Nimlos, W. S. Adney, M.. E. Himmel and M. F. Crowley. Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods Journal of Biological Chemistry (2011) doi

  17. D. L. Mobley, C. I. Bayly, M. D. Cooper, M. R. Shirts, K. A. Dill. Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. Journal of Chemical Theory and Information, 5, 350-358 (2009) doi

  18. M. R. Shirts and J. D. Chodera. Statistically optimal analysis of multiple equilibrium simulations. Journal of Chemical Physics, 129:124105 (2008) doi Accompanying code

  19. K. Zhu, M. R. Shirts, and R. A. Friesner. 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. Journal of Chemical Theory and Computation, 3:2108-2119 (2007) doi

  20. M. R. Shirts, D. L. Mobley, and J. D. Chodera. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. Journal of Physical Chemistry B, 111:13052-13063, (2007) doi

  21. M. R. Shirts, D. L. Mobley, and J. D. Chodera. Alchemical Free Energy Computations: Ready for Prime Time? Annual Reports in Computational Chemistry, 3:41-59 (2007) doi

  22. K. Zhu, M. R. Shirts, R. A. Friesner, and M.P. Jacobson. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. Journal of Chemical Theory and Computation, 3(2),640-648 (2007) doi

  23. G. Jayachandran, M. R. Shirts, S. Park, and V. S. Pande. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. Journal of Chemical Physics, 125, 084901 (2006) doi

  24. E. J. Sorin, Y. M. Rhee, M. R. Shirts, and V. S. Pande. The Solvation Interface is a Determining Factor in Peptide Conformational Preferences. Journal of Molecular Biology, 356, 248 (2006) doi

  25. H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande. Direct calculation of the binding free energies of FKBP ligands. Journal of Chemical Physics, 123, 084108 (2005) doi

  26. M. R. Shirts and V. S. Pande. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. Journal of Chemical Physics 122, 144107 (2005) doi

  27. M. R. Shirts and V. S. Pande. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. Journal of Chemical Physics, 122, 134508 (2005) doi

  28. M. R. Shirts, E. Bair, G. Hooker, and V. S. Pande. Equilibrium free energies from nonequilibrium measurements using maximum likelihood methods. Physical Review Letters 91, 140601 (2003) doi

  29. M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins. Journal of Chemical Physics 119(11), 5740 (2003) doi

  30. V. S. Pande, I. Baker, J. Chapman, S. P. Elmer, S. Khaliq, S. M. Larson, Y. M. Rhee, M. R. Shirts, C. Snow, E. Sorin, B. Zagrovic. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Review for Kollman Memorial Issue, Biopolymers 68 (1), 91-109 (2003) doi

  31. B. Zagrovic, C. D. Snow, M. R. Shirts, and V. S. Pande. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal of Molecular Biology 323, 927-937 (2002) doi

  32. B. Zagrovic, C. Snow, S. Khaliq, M. R. Shirts, and V. S. Pande. Native-like structure in the unfolded state of proteins. Journal of Molecular Biology 323, 153-164 (2002) doi

  33. R. B. Shirts and M. R. Shirts. Deviations from the Boltzmann distribution in small microcanonical quantum systems: Two approximate one-particle energy distributions. Journal of Chemical Physics 117(12), 5564-5575 (2002) doi

  34. M. R. Shirts and V. S. Pande. Mathematical Analysis of Coupled Parallel Simulations. Physical Review Letters 86, 4983-4987 (2001) doi

  35. M. Shirts and V. S. Pande. Screen Savers of the World, Unite! Science 290, 1903-1904 (2000) doi