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Eric J. Sorin, Ph.D. - Publications

Affiliations: 
2007 Stanford University, Palo Alto, CA 
Area:
theoretical methods to understand the physical properties of biological molecules
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21 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Bremer PL, De Boer D, Alvarado W, Martinez X, Sorin EJ. Overcoming the Heuristic Nature of -means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes. Journal of Chemical Information and Modeling. PMID 32383869 DOI: 10.1021/Acs.Jcim.9B01137  0.397
2019 Alvarado W, Ladd Bremer P, Choy A, Dinh HN, Eung A, Gonzalez J, Ly P, Tran T, Nakayama K, Schwans JP, Sorin EJ. Understanding the Enzyme-Ligand Complex: Insights from All-Atom Simulations of Butyrylcholinesterase Inhibition. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 30909811 DOI: 10.1080/07391102.2019.1596836  0.383
2017 Sorin EJ, Alvarado W, Cao S, Radcliffe A, La P, An Y. Ensemble Molecular Dynamics of a Protein-Ligand Complex: Residual Inhibitor Entropy Enhances Drug Potency in Butyrylcholinesterase. Bioenergetics : Open Access. 6. PMID 28944107 DOI: 10.4172/2167-7662.1000145  0.327
2017 Q Nguyen KK, Gomez YK, Bakhom M, Radcliffe A, La P, Rochelle D, Lee JW, Sorin EJ. Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot. Nucleic Acids Research. PMID 28115636 DOI: 10.1093/Nar/Gkx012  0.564
2010 Thompson EJ, DePaul AJ, Patel SS, Sorin EJ. Evaluating molecular mechanical potentials for helical peptides and proteins. Plos One. 5: e10056. PMID 20418937 DOI: 10.1371/Journal.Pone.0010056  0.5
2010 DePaul AJ, Thompson EJ, Patel SS, Haldeman K, Sorin EJ. Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics. Nucleic Acids Research. 38: 4856-67. PMID 20223768 DOI: 10.1093/Nar/Gkq134  0.547
2008 Monticelli L, Sorin EJ, Tieleman DP, Pande VS, Colombo G. Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. Journal of Computational Chemistry. 29: 1740-52. PMID 18307167 DOI: 10.1002/Jcc.20935  0.631
2006 Sorin EJ, Pande VS. Nanotube confinement denatures protein helices. Journal of the American Chemical Society. 128: 6316-7. PMID 16683786 DOI: 10.1021/Ja060917J  0.524
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  0.755
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  0.692
2005 Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS. Unusual compactness of a polyproline type II structure. Proceedings of the National Academy of Sciences of the United States of America. 102: 11698-703. PMID 16085707 DOI: 10.1073/Pnas.0409693102  0.754
2005 Snow CD, Sorin EJ, Rhee YM, Pande VS. How well can simulation predict protein folding kinetics and thermodynamics? Annual Review of Biophysics and Biomolecular Structure. 34: 43-69. PMID 15869383 DOI: 10.1146/Annurev.Biophys.34.040204.144447  0.794
2005 Sorin EJ, Pande VS. Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. Journal of Computational Chemistry. 26: 682-90. PMID 15754305 DOI: 10.1002/Jcc.20208  0.554
2005 Sorin EJ, Rhee YM, Pande VS. Does water play a structural role in the folding of small nucleic acids? Biophysical Journal. 88: 2516-24. PMID 15681648 DOI: 10.1529/Biophysj.104.055087  0.769
2005 Sorin EJ, Pande VS. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophysical Journal. 88: 2472-93. PMID 15665128 DOI: 10.1529/Biophysj.104.051938  0.685
2004 Rhee YM, Sorin EJ, Jayachandran G, Lindahl E, Pande VS. Simulations of the role of water in the protein-folding mechanism. Proceedings of the National Academy of Sciences of the United States of America. 101: 6456-61. PMID 15090647 DOI: 10.1073/Pnas.0307898101  0.782
2004 Sorin EJ, Nakatani BJ, Rhee YM, Jayachandran G, Vishal V, Pande VS. Does native state topology determine the RNA folding mechanism? Journal of Molecular Biology. 337: 789-97. PMID 15033351 DOI: 10.1016/J.Jmb.2004.02.024  0.762
2003 Sorin EJ, Rhee YM, Nakatani BJ, Pande VS. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophysical Journal. 85: 790-803. PMID 12885628 DOI: 10.1016/S0006-3495(03)74520-2  0.782
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  0.678
2002 Sorin EJ, Engelhardt MA, Herschlag D, Pande VS. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. Journal of Molecular Biology. 317: 493-506. PMID 11955005 DOI: 10.1006/Jmbi.2002.5447  0.777
2001 Zagrovic B, Sorin EJ, Pande V. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. Journal of Molecular Biology. 313: 151-69. PMID 11601853 DOI: 10.1006/Jmbi.2001.5033  0.741
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