Aaron Dinner to Models, Molecular
This is a "connection" page, showing publications Aaron Dinner has written about Models, Molecular.
Connection Strength
1.523
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Models of single-molecule experiments with periodic perturbations reveal hidden dynamics in RNA folding. J Phys Chem B. 2009 May 28; 113(21):7579-90.
Score: 0.236
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Apparent directional scanning for DNA repair. Biophys J. 2008 Jan 01; 94(1):47-52.
Score: 0.210
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Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock. Mol Syst Biol. 2020 06; 16(6):e9355.
Score: 0.127
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Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights. Proc Natl Acad Sci U S A. 2018 12 04; 115(49):E11475-E11484.
Score: 0.114
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A metastable state in folding simulations of a protein model. Nat Struct Biol. 1998 Mar; 5(3):236-41.
Score: 0.108
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Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. J Chem Phys. 2014 May 14; 140(18):184114.
Score: 0.083
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CHARMM: the biomolecular simulation program. J Comput Chem. 2009 Jul 30; 30(10):1545-614.
Score: 0.060
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Implications of alternative substrate binding modes for catalysis by uracil-DNA glycosylase: an apparent discrepancy resolved. Biochemistry. 2006 Nov 21; 45(46):13687-96.
Score: 0.050
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Conformational sampling via a self-regulating effective energy surface. J Chem Phys. 2006 May 07; 124(17):174901.
Score: 0.048
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Dynamic coupling between coordinates in a model for biomolecular isomerization. J Chem Phys. 2006 Apr 14; 124(14):144911.
Score: 0.048
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Monte Carlo simulations of biomolecules: The MC module in CHARMM. J Comput Chem. 2006 Jan 30; 27(2):203-16.
Score: 0.047
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Enhancement of diffusion-controlled reaction rates by surface-induced orientational restriction. Biophys J. 2006 Feb 01; 90(3):896-902.
Score: 0.046
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Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B. 2005 Apr 14; 109(14):6769-79.
Score: 0.044
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Temperature-dependent fold-switching mechanism of the circadian clock protein KaiB. Proc Natl Acad Sci U S A. 2024 Dec 17; 121(51):e2412327121.
Score: 0.043
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Grand canonical Monte Carlo simulations of water in protein environments. J Chem Phys. 2004 Oct 01; 121(13):6392-400.
Score: 0.043
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Uracil-DNA glycosylase acts by substrate autocatalysis. Nature. 2001 Oct 18; 413(6857):752-5.
Score: 0.035
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Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci. 2000 Jul; 25(7):331-9.
Score: 0.032
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Understanding beta-hairpin formation. Proc Natl Acad Sci U S A. 1999 Aug 03; 96(16):9068-73.
Score: 0.030
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Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification. Genes Dev. 2018 03 01; 32(5-6):389-401.
Score: 0.027
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Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol. 2012 Jun 03; 19(7):671-6.
Score: 0.018
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Delineation of folding pathways of a ß-sheet miniprotein. J Phys Chem B. 2011 Nov 10; 115(44):13065-74.
Score: 0.017
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Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme. EMBO J. 2010 Dec 01; 29(23):3952-66.
Score: 0.016
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The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A. 2008 Sep 09; 105(36):13586-91.
Score: 0.014
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Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proc Natl Acad Sci U S A. 2003 Nov 25; 100(24):13922-7.
Score: 0.010
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Elastic energy storage in beta-sheets with application to F1-ATPase. Eur Biophys J. 2003 Dec; 32(8):676-83.
Score: 0.010
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One of two unstructured domains of Ii becomes ordered in complexes with MHC class II molecules. Immunity. 1999 Jun; 10(6):761-8.
Score: 0.007