| Year |
Citation |
Score |
| 2024 |
Takaba K, Friedman AJ, Cavender CE, Behara PK, Pulido I, Henry MM, MacDermott-Opeskin H, Iacovella CR, Nagle AM, Payne AM, Shirts MR, Mobley DL, Chodera JD, Wang Y. Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical Science. 15: 12861-12878. PMID 39148808 DOI: 10.1039/d4sc00690a |
0.619 |
|
| 2024 |
Hsu WT, Shirts MR. Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability. Journal of Chemical Theory and Computation. 20: 6062-6081. PMID 39007702 DOI: 10.1021/acs.jctc.4c00484 |
0.362 |
|
| 2024 |
Olehnovics E, Liu YM, Mehio N, Sheikh AY, Shirts MR, Salvalaglio M. Assessing the Accuracy and Efficiency of Free Energy Differences Obtained from Flow-Based Probabilistic Generative Models. Journal of Chemical Theory and Computation. PMID 38984825 DOI: 10.1021/acs.jctc.4c00520 |
0.314 |
|
| 2023 |
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, ... ... Shirts MR, et al. Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation. PMID 37167319 DOI: 10.1021/acs.jctc.3c00039 |
0.714 |
|
| 2022 |
Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. Journal of Chemical Theory and Computation. PMID 35533269 DOI: 10.1021/acs.jctc.1c01268 |
0.711 |
|
| 2022 |
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. Journal of Chemical Theory and Computation. PMID 35507313 DOI: 10.1021/acs.jctc.1c01111 |
0.718 |
|
| 2022 |
Madin OC, Boothroyd S, Messerly RA, Fass J, Chodera JD, Shirts MR. Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. Journal of Chemical Information and Modeling. 62: 874-889. PMID 35129974 DOI: 10.1021/acs.jcim.1c00829 |
0.546 |
|
| 2021 |
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, et al. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. Journal of Chemical Theory and Computation. PMID 34551262 DOI: 10.1021/acs.jctc.1c00571 |
0.721 |
|
| 2021 |
Zhang S, Hahn DF, Shirts MR, Voelz VA. Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies. Journal of Chemical Theory and Computation. PMID 34516130 DOI: 10.1021/acs.jctc.1c00513 |
0.687 |
|
| 2020 |
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 Journal of Computational Molecular Science. 2. PMID 34458687 DOI: 10.33011/livecoms.2.1.18378 |
0.636 |
|
| 2020 |
Abraham NS, Shirts MR. Statistical mechanical approximations to more efficiently determine polymorph free energy differences for small organic molecules. Journal of Chemical Theory and Computation. PMID 32877183 DOI: 10.1021/Acs.Jctc.0C00570 |
0.4 |
|
| 2020 |
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. The Journal of Physical Chemistry. B. PMID 32790365 DOI: 10.1021/Acs.Jpcb.0C05010 |
0.302 |
|
| 2020 |
Coscia BJ, Shirts MR. Capturing Subdiffusive Solute Dynamics and Predicting Selectivity in Nanoscale Pores with Time Series Modeling. Journal of Chemical Theory and Computation. 16: 5456-5473. PMID 32786916 DOI: 10.1021/Acs.Jctc.0C00445 |
0.363 |
|
| 2020 |
Shirts MR, Ferguson AL. Statistically optimal continuous free energy surfaces from biased simulations and multistate reweighting. Journal of Chemical Theory and Computation. PMID 32497425 DOI: 10.1021/Acs.Jctc.0C00077 |
0.421 |
|
| 2020 |
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, et al. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design. PMID 31984465 DOI: 10.1007/S10822-020-00290-5 |
0.693 |
|
| 2020 |
Balasubramanian V, Jensen T, Turilli M, Kasson P, Shirts M, Jha S. Adaptive Ensemble Biomolecular Applications at Scale Sn Computer Science. 1. DOI: 10.1007/s42979-020-0081-1 |
0.518 |
|
| 2019 |
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. The Journal of Chemical Physics. 150: 164112. PMID 31042900 DOI: 10.1063/1.5080431 |
0.346 |
|
| 2019 |
Messerly RA, Soroush Barhaghi M, Potoff JJ, Shirts MR. Histogram-Free Reweighting with Grand Canonical Monte Carlo: Post-simulation Optimization of Non-bonded Potentials for Phase Equilibria Journal of Chemical & Engineering Data. 64: 3701-3717. DOI: 10.1021/Acs.Jced.8B01232 |
0.427 |
|
| 2019 |
Abraham NS, Shirts MR. Adding Anisotropy to the Standard Quasi-Harmonic Approximation Still Fails in Several Ways to Capture Organic Crystal Thermodynamics Crystal Growth & Design. 19: 6911-6924. DOI: 10.1021/Acs.Cgd.9B00547 |
0.366 |
|
| 2018 |
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. The Journal of Physical Chemistry. B. PMID 30521339 DOI: 10.1021/Acs.Jpcb.8B09944 |
0.339 |
|
| 2018 |
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. Journal of Chemical Theory and Computation. PMID 30512951 DOI: 10.1021/Acs.Jctc.8B00821 |
0.6 |
|
| 2018 |
Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Eastman PK. Escaping atom types in force fields using direct chemical perception. Journal of Chemical Theory and Computation. PMID 30351006 DOI: 10.1021/Acs.Jctc.8B00640 |
0.579 |
|
| 2018 |
Abraham NS, Shirts MR. A Thermal Gradient Approach for the Quasi-Harmonic Approximation and its Application to Improved Treatment of Anisotropic Expansion. Journal of Chemical Theory and Computation. PMID 30281302 DOI: 10.1021/Acs.Jctc.8B00460 |
0.366 |
|
| 2018 |
Messerly RA, Shirts MR, Kazakov AF. Uncertainty quantification confirms unreliable extrapolation toward high pressures for united-atom Mie -6 force field. The Journal of Chemical Physics. 149: 114109. PMID 30243285 DOI: 10.1063/1.5039504 |
0.337 |
|
| 2018 |
Merz PT, Shirts MR. Testing for physical validity in molecular simulations. Plos One. 13: e0202764. PMID 30188933 DOI: 10.1371/Journal.Pone.0202764 |
0.415 |
|
| 2018 |
Messerly RA, Razavi SM, Shirts MR. Configuration-Sampling-Based Surrogate Models for Rapid Parameterization of Non-bonded Interactions. Journal of Chemical Theory and Computation. PMID 29727563 DOI: 10.1021/Acs.Jctc.8B00223 |
0.403 |
|
| 2018 |
Schieber NP, Dybeck EC, Shirts MR. Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams. The Journal of Chemical Physics. 148: 144104. PMID 29655343 DOI: 10.1063/1.5013273 |
0.367 |
|
| 2017 |
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. Journal of Chemical and Engineering Data. 62: 1559-1569. PMID 29056756 DOI: 10.1021/Acs.Jced.7B00104 |
0.67 |
|
| 2017 |
Dybeck EC, Abraham NS, Schieber NP, Shirts MR. Capturing Entropic Contributions to Temperature-Mediated Polymorphic Transformations Through Molecular Modeling Crystal Growth & Design. 17: 1775-1787. DOI: 10.1021/Acs.Cgd.6B01762 |
0.377 |
|
| 2017 |
Basconi JE, Carta G, Shirts MR. Effects of protein properties on adsorption and transport in polymer-grafted ion exchangers: A multiscale modeling study Aiche Journal. 63: 4564-4575. DOI: 10.1002/Aic.15798 |
0.315 |
|
| 2016 |
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. Journal of Computer-Aided Molecular Design. PMID 27787702 DOI: 10.1007/S10822-016-9977-1 |
0.43 |
|
| 2016 |
Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. 30: 927-944. PMID 27677750 DOI: 10.1007/S10822-016-9954-8 |
0.356 |
|
| 2016 |
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? Journal of Computer-Aided Molecular Design. PMID 27658802 DOI: 10.1007/S10822-016-9974-4 |
0.424 |
|
| 2016 |
Dybeck EC, Schieber NP, Shirts MR. The Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials. Journal of Chemical Theory and Computation. PMID 27341280 DOI: 10.1021/Acs.Jctc.6B00397 |
0.381 |
|
| 2016 |
Dybeck EC, König G, Brooks BR, Shirts MR. A Comparison of Methods to Reweight from Classical Molecular Simulations to QM/MM Potentials. Journal of Chemical Theory and Computation. PMID 26928941 DOI: 10.1021/Acs.Jctc.5B01188 |
0.408 |
|
| 2016 |
Naden LN, Shirts MR. Rapid Computation of Thermodynamic Properties Over Multidimensional Nonbonded Parameter Spaces using Adaptive Multistate Reweighting. Journal of Chemical Theory and Computation. PMID 26849009 DOI: 10.1021/Acs.Jctc.5B00869 |
0.422 |
|
| 2015 |
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. Journal of Chemical Theory and Computation. 11: 1347. PMID 26579779 DOI: 10.1021/Acs.Jctc.5B00154 |
0.361 |
|
| 2015 |
Naden LN, Shirts MR. Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions. Journal of Chemical Theory and Computation. 11: 2536-49. PMID 26575553 DOI: 10.1021/Ct501047E |
0.36 |
|
| 2015 |
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 : the Acs Journal of Surfaces and Colloids. 31: 7980-90. PMID 26110823 DOI: 10.1021/Acs.Langmuir.5B00842 |
0.315 |
|
| 2015 |
Klimovich PV, Shirts MR, Mobley DL. Guidelines for the analysis of free energy calculations. Journal of Computer-Aided Molecular Design. 29: 397-411. PMID 25808134 DOI: 10.1007/S10822-015-9840-9 |
0.44 |
|
| 2014 |
Naden LN, Pham TT, Shirts MR. Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites. Journal of Chemical Theory and Computation. 10: 1128-49. PMID 26580188 DOI: 10.1021/Ct4009188 |
0.412 |
|
| 2014 |
Zhong ED, Shirts MR. Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations. Langmuir : the Acs Journal of Surfaces and Colloids. 30: 4952-61. PMID 24716898 DOI: 10.1021/La500511P |
0.424 |
|
| 2014 |
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. Journal of Computer-Aided Molecular Design. 28: 401-15. PMID 24610238 DOI: 10.1007/S10822-014-9716-4 |
0.512 |
|
| 2014 |
Basconi JE, Carta G, Shirts MR. Multiscale modeling of protein adsorption and transport in macroporous and polymer-grafted ion exchangers Aiche Journal. 60: 3888-3901. DOI: 10.1002/Aic.14621 |
0.315 |
|
| 2013 |
Shirts MR. Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles. Journal of Chemical Theory and Computation. 9: 909-26. PMID 26588735 DOI: 10.1021/Ct300688P |
0.396 |
|
| 2013 |
Basconi JE, Shirts MR. Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 9: 2887-99. PMID 26583973 DOI: 10.1021/Ct400109A |
0.328 |
|
| 2013 |
Paliwal H, Shirts MR. Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions. Journal of Chemical Theory and Computation. 9: 4700-17. PMID 26583389 DOI: 10.1021/Ct4005068 |
0.457 |
|
| 2013 |
Wang K, Chodera JD, Yang Y, Shirts MR. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. Journal of Computer-Aided Molecular Design. 27: 989-1007. PMID 24297454 DOI: 10.1007/S10822-013-9689-8 |
0.624 |
|
| 2013 |
Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT. Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy. Journal of the American Chemical Society. 135: 18831-9. PMID 24279927 DOI: 10.1021/Ja407287F |
0.367 |
|
| 2013 |
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. The Journal of Chemical Physics. 138: 154108. PMID 23614413 DOI: 10.1063/1.4801332 |
0.415 |
|
| 2013 |
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 (Oxford, England). 29: 845-54. PMID 23407358 DOI: 10.1093/Bioinformatics/Btt055 |
0.688 |
|
| 2013 |
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, et al. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. Journal of Chemical Theory and Computation. 9: 461-469. PMID 23316124 DOI: 10.1021/Ct300857J |
0.781 |
|
| 2013 |
Shirts MR, Mobley DL. An introduction to best practices in free energy calculations. Methods in Molecular Biology (Clifton, N.J.). 924: 271-311. PMID 23034753 DOI: 10.1007/978-1-62703-017-5_11 |
0.469 |
|
| 2013 |
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, et al. OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation Journal of Chemical Theory and Computation. 9: 461-469. DOI: 10.1021/ct300857j |
0.784 |
|
| 2013 |
Wang K, Yang Y, Chodera JD, Shirts MR. Identifying ligand binding sites and poses using Hamiltonian replica exchange molecular dynamics: Model systems and a validation study using the astex diverse set Engineering Sciences and Fundamentals 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 2: 622. |
0.544 |
|
| 2012 |
Fuller JC, Jackson RM, Shirts MR. Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities. The Journal of Physical Chemistry. B. 116: 10856-69. PMID 22920218 DOI: 10.1021/Jp209041X |
0.433 |
|
| 2012 |
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. 7: e43253. PMID 22916232 DOI: 10.1371/Journal.Pone.0043253 |
0.389 |
|
| 2012 |
Pham TT, Shirts MR. Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase. The Journal of Chemical Physics. 136: 124120. PMID 22462848 DOI: 10.1063/1.3697833 |
0.413 |
|
| 2012 |
Shirts MR. Best practices in free energy calculations for drug design. Methods in Molecular Biology (Clifton, N.J.). 819: 425-67. PMID 22183551 DOI: 10.1007/978-1-61779-465-0_26 |
0.457 |
|
| 2011 |
Paliwal H, Shirts MR. 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: 4115-34. PMID 26598357 DOI: 10.1021/Ct2003995 |
0.431 |
|
| 2011 |
Chodera JD, Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. The Journal of Chemical Physics. 135: 194110. PMID 22112069 DOI: 10.1063/1.3660669 |
0.64 |
|
| 2011 |
Pham TT, Shirts MR. Identifying low variance pathways for free energy calculations of molecular transformations in solution phase. The Journal of Chemical Physics. 135: 034114. PMID 21786994 DOI: 10.1063/1.3607597 |
0.429 |
|
| 2011 |
Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS. Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. The Journal of Chemical Physics. 134: 244107. PMID 21721612 DOI: 10.1063/1.3592152 |
0.772 |
|
| 2011 |
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. The Journal of Biological Chemistry. 286: 18161-9. PMID 21454590 DOI: 10.1074/Jbc.M110.212076 |
0.423 |
|
| 2011 |
Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. Alchemical free energy methods for drug discovery: progress and challenges. Current Opinion in Structural Biology. 21: 150-60. PMID 21349700 DOI: 10.1016/J.Sbi.2011.01.011 |
0.669 |
|
| 2009 |
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. Journal of Chemical Theory and Computation. 5: 350-358. PMID 20150953 DOI: 10.1021/Ct800409D |
0.463 |
|
| 2008 |
Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics. 129: 124105. PMID 19045004 DOI: 10.1063/1.2978177 |
0.611 |
|
| 2008 |
Shirts MR, Pande VS. Erratum: “Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration” [J. Chem. Phys. 122, 144107 (2005)] The Journal of Chemical Physics. 129: 229901. DOI: 10.1063/1.3033406 |
0.565 |
|
| 2008 |
Shirts MR, Chodera JD. Statistically optimal free energy estimates from sparsely chosen states Aiche Annual Meeting, Conference Proceedings. |
0.55 |
|
| 2007 |
Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. Journal of Chemical Theory and Computation. 3: 640-8. PMID 26637042 DOI: 10.1021/Ct600129F |
0.528 |
|
| 2007 |
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. Journal of Chemical Theory and Computation. 3: 2108-19. PMID 26636204 DOI: 10.1021/Ct700166F |
0.536 |
|
| 2007 |
Shirts MR, Mobley DL, Chodera JD, Pande VS. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. The Journal of Physical Chemistry. B. 111: 13052-63. PMID 17949030 DOI: 10.1021/Jp0735987 |
0.752 |
|
| 2007 |
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 Journal of Chemical Theory and Computation. 3: 2108-2119. DOI: 10.1021/ct700166f |
0.414 |
|
| 2007 |
Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale optimization of a truncated newton minimization algorithm and application to proteins and protein-ligand complexes Journal of Chemical Theory and Computation. 3: 640-648. DOI: 10.1021/ct600129f |
0.44 |
|
| 2007 |
Shirts MR, Mobley DL, Chodera JD. Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time? Annual Reports in Computational Chemistry. 3: 41-59. DOI: 10.1016/S1574-1400(07)03004-6 |
0.661 |
|
| 2006 |
Jayachandran G, Shirts MR, Park S, Pande VS. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. The Journal of Chemical Physics. 125: 084901. PMID 16965051 DOI: 10.1063/1.2221680 |
0.781 |
|
| 2006 |
Sorin EJ, Rhee YM, Shirts MR, Pande VS. The solvation interface is a determining factor in peptide conformational preferences. Journal of Molecular Biology. 356: 248-56. PMID 16364361 DOI: 10.1016/J.Jmb.2005.11.058 |
0.758 |
|
| 2005 |
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. The Journal of Chemical Physics. 123: 084108. PMID 16164283 DOI: 10.1063/1.1999637 |
0.764 |
|
| 2005 |
Shirts MR, Pande VS. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. The Journal of Chemical Physics. 122: 144107. PMID 15847516 DOI: 10.1063/1.1873592 |
0.59 |
|
| 2005 |
Shirts MR, Pande VS. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. The Journal of Chemical Physics. 122: 134508. PMID 15847482 DOI: 10.1063/1.1877132 |
0.61 |
|
| 2003 |
Shirts MR, Bair E, Hooker G, Pande VS. Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. Physical Review Letters. 91: 140601. PMID 14611511 DOI: 10.1103/Physrevlett.91.140601 |
0.532 |
|
| 2003 |
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. 68: 91-109. PMID 12579582 DOI: 10.1002/Bip.10219 |
0.736 |
|
| 2003 |
Shirts MR, Pitera JW, Swope WC, Pande VS. 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: 5740-5761. DOI: 10.1063/1.1587119 |
0.764 |
|
| 2002 |
Zagrovic B, Snow CD, Shirts MR, Pande VS. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal of Molecular Biology. 323: 927-37. PMID 12417204 DOI: 10.1016/S0022-2836(02)00997-X |
0.805 |
|
| 2002 |
Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS. Native-like mean structure in the unfolded ensemble of small proteins. Journal of Molecular Biology. 323: 153-64. PMID 12368107 DOI: 10.1016/S0022-2836(02)00888-4 |
0.787 |
|
| 2002 |
Shirts RB, Shirts MR. Deviations from the Boltzmann distribution in small microcanonical quantum systems: Two approximate one-particle energy distributions Journal of Chemical Physics. 117: 5564-5575. DOI: 10.1063/1.1503306 |
0.333 |
|
| 2002 |
Zagrovic B, Snow CD, Shirts MR, Pande VS. Corrigendum to “Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing” Journal of Molecular Biology. 324: 1051. DOI: 10.1016/S0022-2836(02)01244-5 |
0.759 |
|
| 2001 |
Shirts MR, Pande VS. Mathematical analysis of coupled parallel simulations. Physical Review Letters. 86: 4983-7. PMID 11384401 DOI: 10.1103/Physrevlett.86.4983 |
0.561 |
|
| 2000 |
Shirts M, Pande VS. COMPUTING: Screen Savers of the World Unite! Science (New York, N.Y.). 290: 1903-4. PMID 17742054 DOI: 10.1126/Science.290.5498.1903 |
0.519 |
|
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