Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations von Sorin, Eric J., Pande, Vijay S.

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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... von Bains, Gursharan K, Kim, Sea H, Sorin, Eric J, Narayanaswami, Vasanthy

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A Comprehensive Review of Cholinesterase Modeling and Simulation von De Boer, Danna, Nguyen, Nguyet, Mao, Jia, Moore, Jessica, Sorin, Eric J

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A Hands-On Collaboration-Ready Single- or Interdisciplinary Computational Exercise in Molecular Recognition and Drug Design von Allen, Patrick, Nguyen, Nguyet, Humphrey, Nicholas D., Mao, Jia, Chavez-Bonilla, Daniel, Sorin, Eric J.

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Direct calculation of the binding free energies of FKBP ligands von Fujitani, Hideaki, Tanida, Yoshiaki, Ito, Masakatsu, Jayachandran, Guha, Snow, Christopher D., Shirts, Michael R., Sorin, Eric J., Pande, Vijay S.

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Simulations of the Role of Water in the Protein-Folding Mechanism von Rhee, Young Min, Sorin, Eric J., Jayachandran, Guha, Lindahl, Erik, Pande, Vijay S., Scheraga, Harold A.

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Evaluating molecular mechanical potentials for helical peptides and proteins von Thompson, Erik J, DePaul, Allison J, Patel, Sarav S, Sorin, Eric J

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Unusual Compactness of a Polyproline Type II Structure von Zagrovic, Bojan, Lipfert, Jan, Sorin, Eric J., Millett, Ian S., van Gunsteren, Wilfred F., Doniach, Sebastian, Pande, Vijay S., Levitt, Michael

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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing von Pande, Vijay S., Baker, Ian, Chapman, Jarrod, Elmer, Sidney P., Khaliq, Siraj, Larson, Stefan M., Rhee, Young Min, Shirts, Michael R., Snow, Christopher D., Sorin, Eric J., Zagrovic, Bojan

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Does Water Play a Structural Role in the Folding of Small Nucleic Acids? von Sorin, Eric J., Rhee, Young Min, Pande, Vijay S.

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Overcoming the Heuristic Nature of k -Means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes von Bremer, Parker Ladd, De Boer, Danna, Alvarado, Walter, Martinez, Xavier, Sorin, Eric J

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Energetically unfavorable protein angles: Exploration of a conserved dihedral angle in triosephosphate isomerase von Allen, Patrick W., Cook, Jordan A., Colquhoun, Anh N., Sorin, Eric J., Tapavicza, Enrico, Schwans, Jason P.

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Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics von DePaul, Allison J, Thompson, Erik J, Patel, Sarav S, Haldeman, Kristin, Sorin, Eric J

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Synthesis, biochemical evaluation, and molecular modeling studies of aryl and arylalkyl di-n-butyl phosphates, effective butyrylcholinesterase inhibitors von Nakayama, Kensaku, Schwans, Jason P., Sorin, Eric J., Tran, Trina, Gonzalez, Jeannette, Arteaga, Elvis, McCoy, Sean, Alvarado, Walter

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Nanotube Confinement Denatures Protein Helices von Sorin, Eric J, Pande, Vijay S

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Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot von Q Nguyen, Khai K, Gomez, Yessica K, Bakhom, Mona, Radcliffe, Amethyst, La, Phuc, Rochelle, Dakota, Lee, Ji Won, Sorin, Eric J

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Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories von Monticelli, Luca, Sorin, Eric J, Tieleman, D. Peter, Pande, Vijay S, Colombo, Giorgio

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Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling von Sorin, Eric J., Pande, Vijay S.

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Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations von Sorin, Eric J., Rhee, Young Min, Nakatani, Bradley J., Pande, Vijay S.

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RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop von Sorin, Eric J, Engelhardt, Mark A, Herschlag, Daniel, Pande, Vijay S

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