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Items: 1 to 50 of 63

1.

Chemically Selective Transport in a Cross-Linked HII Phase Lyotropic Liquid Crystal Membrane.

Coscia BJ, Shirts MR.

J Phys Chem B. 2019 Jul 25;123(29):6314-6330. doi: 10.1021/acs.jpcb.9b04472. Epub 2019 Jul 11.

PMID:
31247136
3.

Understanding the Nanoscale Structure of Inverted Hexagonal Phase Lyotropic Liquid Crystal Polymer Membranes.

Coscia BJ, Yelk J, Glaser MA, Gin DL, Feng X, Shirts MR.

J Phys Chem B. 2019 Jan 10;123(1):289-309. doi: 10.1021/acs.jpcb.8b09944. Epub 2018 Dec 24.

PMID:
30521339
4.

Toward Learned Chemical Perception of Force Field Typing Rules.

Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL.

J Chem Theory Comput. 2019 Jan 8;15(1):402-423. doi: 10.1021/acs.jctc.8b00821. Epub 2018 Dec 24.

PMID:
30512951
5.

Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK.

J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30.

6.

Thermal Gradient Approach for the Quasi-harmonic Approximation and Its Application to Improved Treatment of Anisotropic Expansion.

Abraham NS, Shirts MR.

J Chem Theory Comput. 2018 Nov 13;14(11):5904-5919. doi: 10.1021/acs.jctc.8b00460. Epub 2018 Oct 26.

PMID:
30281302
7.

Uncertainty quantification confirms unreliable extrapolation toward high pressures for united-atom Mie λ-6 force field.

Messerly RA, Shirts MR, Kazakov AF.

J Chem Phys. 2018 Sep 21;149(11):114109. doi: 10.1063/1.5039504.

PMID:
30243285
8.

Testing for physical validity in molecular simulations.

Merz PT, Shirts MR.

PLoS One. 2018 Sep 6;13(9):e0202764. doi: 10.1371/journal.pone.0202764. eCollection 2018.

9.

Configuration-Sampling-Based Surrogate Models for Rapid Parameterization of Non-Bonded Interactions.

Messerly RA, Razavi SM, Shirts MR.

J Chem Theory Comput. 2018 Jun 12;14(6):3144-3162. doi: 10.1021/acs.jctc.8b00223. Epub 2018 May 23.

PMID:
29727563
10.

Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams.

Schieber NP, Dybeck EC, Shirts MR.

J Chem Phys. 2018 Apr 14;148(14):144104. doi: 10.1063/1.5013273.

PMID:
29655343
11.

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL.

J Chem Eng Data. 2017 May 11;62(5):1559-1569. doi: 10.1021/acs.jced.7b00104. Epub 2017 Apr 24.

12.

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED.

J Comput Aided Mol Des. 2017 Aug;31(8):777. doi: 10.1007/s10822-017-0043-4. No abstract available.

13.

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED.

J Comput Aided Mol Des. 2017 Jan;31(1):147-161. doi: 10.1007/s10822-016-9977-1. Epub 2016 Oct 27. Erratum in: J Comput Aided Mol Des. 2017 Jul 27;:.

14.

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL.

J Comput Aided Mol Des. 2016 Nov;30(11):927-944. doi: 10.1007/s10822-016-9954-8. Epub 2016 Sep 27.

15.

Overview of the SAMPL5 host-guest challenge: Are we doing better?

Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK.

J Comput Aided Mol Des. 2017 Jan;31(1):1-19. doi: 10.1007/s10822-016-9974-4. Epub 2016 Sep 22. Review.

16.

Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials.

Dybeck EC, Schieber NP, Shirts MR.

J Chem Theory Comput. 2016 Aug 9;12(8):3491-505. doi: 10.1021/acs.jctc.6b00397. Epub 2016 Jul 25.

PMID:
27341280
17.

Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.

Dybeck EC, König G, Brooks BR, Shirts MR.

J Chem Theory Comput. 2016 Apr 12;12(4):1466-80. doi: 10.1021/acs.jctc.5b01188. Epub 2016 Mar 23.

18.

Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting.

Naden LN, Shirts MR.

J Chem Theory Comput. 2016 Apr 12;12(4):1806-23. doi: 10.1021/acs.jctc.5b00869. Epub 2016 Feb 29.

PMID:
26849009
19.

Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations.

Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA.

J Chem Theory Comput. 2015 Mar 10;11(3):1347. doi: 10.1021/acs.jctc.5b00154. No abstract available.

20.
21.

Identifying Differences and Similarities in Static and Dynamic Contact Angles between Nanoscale and Microscale Textured Surfaces Using Molecular Dynamics Simulations.

Slovin MR, Shirts MR.

Langmuir. 2015 Jul 28;31(29):7980-90. doi: 10.1021/acs.langmuir.5b00842. Epub 2015 Jul 14.

PMID:
26110823
22.

Guidelines for the analysis of free energy calculations.

Klimovich PV, Shirts MR, Mobley DL.

J Comput Aided Mol Des. 2015 May;29(5):397-411. doi: 10.1007/s10822-015-9840-9. Epub 2015 Mar 26.

23.

Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study.

Basconi JE, Carta G, Shirts MR.

Langmuir. 2015 Apr 14;31(14):4176-87. doi: 10.1021/la504768g. Epub 2015 Mar 30.

PMID:
25785668
24.

Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations.

Zhong ED, Shirts MR.

Langmuir. 2014 May 6;30(17):4952-61. doi: 10.1021/la500511p. Epub 2014 Apr 22.

PMID:
24716898
25.

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations.

Monroe JI, Shirts MR.

J Comput Aided Mol Des. 2014 Apr;28(4):401-15. doi: 10.1007/s10822-014-9716-4. Epub 2014 Mar 8.

PMID:
24610238
26.

Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites.

Naden LN, Pham TT, Shirts MR.

J Chem Theory Comput. 2014 Mar 11;10(3):1128-49. doi: 10.1021/ct4009188.

PMID:
26580188
27.

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.

Wang K, Chodera JD, Yang Y, Shirts MR.

J Comput Aided Mol Des. 2013 Dec;27(12):989-1007. doi: 10.1007/s10822-013-9689-8. Epub 2013 Dec 3.

28.

Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy.

Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT.

J Am Chem Soc. 2013 Dec 18;135(50):18831-9. doi: 10.1021/ja407287f. Epub 2013 Dec 5.

PMID:
24279927
29.

Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions.

Paliwal H, Shirts MR.

J Chem Theory Comput. 2013 Nov 12;9(11):4700-17. doi: 10.1021/ct4005068. Epub 2013 Oct 17.

PMID:
26583389
30.

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations.

Basconi JE, Shirts MR.

J Chem Theory Comput. 2013 Jul 9;9(7):2887-99. doi: 10.1021/ct400109a. Epub 2013 Jun 3.

PMID:
26583973
31.

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

Monroe JI, El-Nahal WG, Shirts MR.

Proteins. 2014 Jan;82(1):130-44. doi: 10.1002/prot.24346. Epub 2013 Sep 17.

PMID:
23775803
33.

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.

Bioinformatics. 2013 Apr 1;29(7):845-54. doi: 10.1093/bioinformatics/btt055. Epub 2013 Feb 13.

34.

Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles.

Shirts MR.

J Chem Theory Comput. 2013 Feb 12;9(2):909-26. doi: 10.1021/ct300688p. Epub 2013 Jan 10.

PMID:
26588735
35.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

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.

J Chem Theory Comput. 2013 Jan 8;9(1):461-469. Epub 2012 Oct 18.

36.

An introduction to best practices in free energy calculations.

Shirts MR, Mobley DL.

Methods Mol Biol. 2013;924:271-311. doi: 10.1007/978-1-62703-017-5_11.

PMID:
23034753
37.

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

Fuller JC, Jackson RM, Shirts MR.

J Phys Chem B. 2012 Sep 6;116(35):10856-69. doi: 10.1021/jp209041x. Epub 2012 Aug 27.

PMID:
22920218
38.

Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.

Fuller JC, Jackson RM, Edwards TA, Wilson AJ, Shirts MR.

PLoS One. 2012;7(8):e43253. doi: 10.1371/journal.pone.0043253. Epub 2012 Aug 20.

39.

Product binding varies dramatically between processive and nonprocessive cellulase enzymes.

Bu L, Nimlos MR, Shirts MR, Ståhlberg J, Himmel ME, Crowley MF, Beckham GT.

J Biol Chem. 2012 Jul 13;287(29):24807-13. doi: 10.1074/jbc.M112.365510. Epub 2012 May 30.

40.

Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase.

Pham TT, Shirts MR.

J Chem Phys. 2012 Mar 28;136(12):124120. doi: 10.1063/1.3697833.

PMID:
22462848
41.

Best practices in free energy calculations for drug design.

Shirts MR.

Methods Mol Biol. 2012;819:425-67. doi: 10.1007/978-1-61779-465-0_26.

PMID:
22183551
42.

A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods.

Paliwal H, Shirts MR.

J Chem Theory Comput. 2011 Dec 13;7(12):4115-34. doi: 10.1021/ct2003995. Epub 2011 Nov 14.

PMID:
26598357
43.

Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.

Chodera JD, Shirts MR.

J Chem Phys. 2011 Nov 21;135(19):194110. doi: 10.1063/1.3660669.

PMID:
22112069
44.

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.

Pharm Res. 2012 Jan;29(1):236-50. doi: 10.1007/s11095-011-0538-y. Epub 2011 Jul 30.

PMID:
21805212
45.

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.

Pham TT, Shirts MR.

J Chem Phys. 2011 Jul 21;135(3):034114. doi: 10.1063/1.3607597.

PMID:
21786994
46.

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.

Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS.

J Chem Phys. 2011 Jun 28;134(24):244107. doi: 10.1063/1.3592152.

47.

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.

J Biol Chem. 2011 May 20;286(20):18161-9. doi: 10.1074/jbc.M110.212076. Epub 2011 Mar 24.

48.

Alchemical free energy methods for drug discovery: progress and challenges.

Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS.

Curr Opin Struct Biol. 2011 Apr;21(2):150-60. doi: 10.1016/j.sbi.2011.01.011. Epub 2011 Feb 23. Review.

49.

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations.

Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA.

J Chem Theory Comput. 2009 Feb 10;5(2):350-358.

50.

Statistically optimal analysis of samples from multiple equilibrium states.

Shirts MR, Chodera JD.

J Chem Phys. 2008 Sep 28;129(12):124105. doi: 10.1063/1.2978177.

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