 Connection
Michael Shirts to Molecular Dynamics Simulation
This is a "connection" page, showing publications Michael Shirts has written about Molecular Dynamics Simulation.
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Connection Strength |
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7.082 |
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Davel CM, Bernat T, Wagner JR, Shirts MR. Parameterization of General Organic Polymers within the Open Force Field Framework. J Chem Inf Model. 2024 02 26; 64(4):1290-1305.
Score: 0.765
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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.
Score: 0.746
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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.
Score: 0.699
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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.
Score: 0.678
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Merz PT, Shirts MR. Testing for physical validity in molecular simulations. PLoS One. 2018; 13(9):e0202764.
Score: 0.526
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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.
Score: 0.462
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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.
Score: 0.444
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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.
Score: 0.414
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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.
Score: 0.385
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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.
Score: 0.378
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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.
Score: 0.346
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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.
Score: 0.328
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Leonard AC, Friedman AJ, Chayer R, Petersen BM, Woojuh J, Xing Z, Cutler SR, Kaar JL, Shirts MR, Whitehead TA. Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design. ACS Chem Biol. 2024 08 16; 19(8):1757-1772.
Score: 0.197
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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.
Score: 0.134
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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.
Score: 0.115
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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.
Score: 0.104
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Zhong ED, Shirts MR. Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations. Langmuir. 2014 May 06; 30(17):4952-61.
Score: 0.097
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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.
Score: 0.093
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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.
Score: 0.089
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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.
Score: 0.080
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Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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