 Connection
Michael Shirts to Proteins
This is a "connection" page, showing publications Michael Shirts has written about Proteins.
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Connection Strength |
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1.521 |
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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: 0.321
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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: 0.270
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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: 0.133
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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.
Score: 0.128
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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.
Score: 0.126
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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.
Score: 0.121
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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.
Score: 0.113
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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.
Score: 0.101
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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: 0.080
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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.
Score: 0.040
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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.
Score: 0.031
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Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS. Native-like mean structure in the unfolded ensemble of small proteins. J Mol Biol. 2002 Oct 11; 323(1):153-64.
Score: 0.030
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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. 2013 Apr 01; 29(7):845-54.
Score: 0.016
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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.
Score: 0.014
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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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