Eric J. Sorin, Ph.D. - Publications

2007 Stanford University, Palo Alto, CA 
theoretical methods to understand the physical properties of biological molecules

16/26 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
2012 Bains GK, Kim SH, Sorin EJ, Narayanaswami V. The extent of pyrene excimer fluorescence emission is a reflector of distance and flexibility: analysis of the segment linking the LDL receptor-binding and tetramerization domains of apolipoprotein E3. Biochemistry. 51: 6207-19. PMID 22779734 DOI: 10.1021/Bi3005285  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
Low-probability matches
2021 De Boer D, Nguyen N, Mao J, Moore J, Sorin EJ. A Comprehensive Review of Cholinesterase Modeling and Simulation. Biomolecules. 11. PMID 33920972 DOI: 10.3390/biom11040580  0.01
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  0.01
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  0.01
2018 Humphrey N, Sanchez M, Chung C, Sorin E. Computational Study of Butyrylcholinesterase Inhibition by Aryl Alkyl Cholinyl Phosphorus Derivatives Biophysical Journal. 114: 680a. DOI: 10.1016/J.Bpj.2017.11.3667  0.01
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  0.01
2017 Nakayama K, Schwans JP, Sorin EJ, Tran T, Gonzalez J, Arteaga E, McCoy S, Alvarado W. Synthesis, biochemical evaluation, and molecular modeling studies of aryl and arylalkyl di-n-butyl phosphates, effective butyrylcholinesterase inhibitors. Bioorganic & Medicinal Chemistry. PMID 28416102 DOI: 10.1016/J.Bmc.2017.04.002  0.01
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  0.01
2014 Radcliffe A, Cao S, Pham B, La P, Wang R, Sorin E. Investigating the Folding Dynamics of RNA Pseudoknot Structural Motif via Massively Parallel Molecular Dynamics Biophysical Journal. 106: 804a. DOI: 10.1016/j.bpj.2013.11.4406  0.01
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  0.01
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  0.48
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