Search Results - "Lupyan, Dmitry"

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins by Harder, Edward, Damm, Wolfgang, Maple, Jon, Wu, Chuanjie, Reboul, Mark, Xiang, Jin Yu, Wang, Lingle, Lupyan, Dmitry, Dahlgren, Markus K, Knight, Jennifer L, Kaus, Joseph W, Cerutti, David S, Krilov, Goran, Jorgensen, William L, Abel, Robert, Friesner, Richard A

“…The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version…”
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Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field by Wang, Lingle, Wu, Yujie, Deng, Yuqing, Kim, Byungchan, Pierce, Levi, Krilov, Goran, Lupyan, Dmitry, Robinson, Shaughnessy, Dahlgren, Markus K, Greenwood, Jeremy, Romero, Donna L, Masse, Craig, Knight, Jennifer L, Steinbrecher, Thomas, Beuming, Thijs, Damm, Wolfgang, Harder, Ed, Sherman, Woody, Brewer, Mark, Wester, Ron, Murcko, Mark, Frye, Leah, Farid, Ramy, Lin, Teng, Mobley, David L, Jorgensen, William L, Berne, Bruce J, Friesner, Richard A, Abel, Robert

“…Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited…”
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Phosphoinositide-mediated gating of inwardly rectifying K(+) channels by Logothetis, Diomedes E, Jin, Taihao, Lupyan, Dmitry, Rosenhouse-Dantsker, Avia

“…Phosphoinositides, such as phosphatidylinositol-bisphosphate (PIP(2)), control the activity of many ion channels in yet undefined ways. Inwardly, rectifying…”
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Diverse Kir modulators act in close proximity to residues implicated in phosphoinositide binding by Diomedes E. Logothetis, Dmitry Lupyan, Avia Rosenhouse-Dantsker

“…Inwardly rectifying potassium (Kir) channels were the first shown to be directly activated by phosphoinositides in general and phosphatidylinositol…”
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An Analysis of Core Deformations in Protein Superfamilies by Leo-Macias, Alejandra, Lopez-Romero, Pedro, Lupyan, Dmitry, Zerbino, Daniel, Ortiz, Angel R.

“…An analysis is presented on how structural cores modify their shape across homologous proteins, and whether or not a relationship exists between these…”
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A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP2 by Lupyan, Dmitry, Mezei, Mihaly, Logothetis, Diomedes E., Osman, Roman

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Improving the Accuracy of Protein Thermostability Predictions for Single Point Mutations by Duan, Jianxin, Lupyan, Dmitry, Wang, Lingle

“…Accurately predicting the protein thermostability changes upon single point mutations in silico is a challenge that has implications for understanding diseases…”
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Target‐template relationships in protein structure prediction and their effect on the accuracy of thermostability calculations by Lihan, Muyun, Lupyan, Dmitry, Oehme, Daniel

“…Improving protein thermostability has been a labor‐ and time‐consuming process in industrial applications of protein engineering. Advances in computational…”
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Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics by Yu, Haoyu S, Gao, Cen, Lupyan, Dmitry, Wu, Yujie, Kimura, Takayuki, Wu, Chuanjie, Jacobson, Leif, Harder, Edward, Abel, Robert, Wang, Lingle

“…Covalent inhibitors have emerged as an important drug class in recent years, largely due to their many unique advantages as compared to noncovalent inhibitors,…”
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A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor by Lyman, Edward, Higgs, Chris, Kim, Byungchan, Lupyan, Dmitry, Shelley, John C., Farid, Ramy, Voth, Gregory A.

“…The function of G-protein-coupled receptors is tightly modulated by the lipid environment. Long-timescale molecular dynamics simulations (totaling ∼3 μs) of…”
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A molecular dynamics investigation of lipid bilayer perturbation by PIP2 by Lupyan, Dmitry, Mezei, Mihaly, Logothetis, Diomedes E, Osman, Roman

“…Phosphoinositides like phosphatidylinositol 4,5-bisphosphate (PIP(2)) are negatively charged lipids that play a pivotal role in membrane trafficking, signal…”
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Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment by Kufareva, Irina, Rueda, Manuel, Katritch, Vsevolod, Stevens, Raymond C., Abagyan, Ruben

“…The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The…”
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A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor by Lyman, Edward, Higgs, Chris, Kim, Byungchan, Lupyan, Dmitry, Shelley, John C, Farid, Ramy, Voth, Gregory A

“…The function of G-protein-coupled receptors is tightly modulated by the lipid environment. Long-timescale molecular dynamics simulations (totaling…”
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Close intramolecular sulfur–oxygen contacts: modified force field parameters for improved conformation generation by Lupyan, Dmitry, Abramov, Yuriy A., Sherman, Woody

“…The Cambridge Structural Database (CSD) offers an excellent data source to study small molecule conformations and molecular interactions. We have analyzed 130…”
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A new progressive-iterative algorithm for multiple structure alignment by Lupyan, Dmitry, Leo-Macias, Alejandra, Ortiz, Angel R.

“…Motivation: Multiple structure alignments are becoming important tools in many aspects of structural bioinformatics. The current explosion in the number of…”
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Erratum to: Close intramolecular sulfur–oxygen contacts: modified force field parameters for improved conformation generation by Lupyan, Dmitry, Abramov, Yuriy A., Sherman, Woody

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A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP sub(2) by Lupyan, Dmitry, Mezei, Mihaly, Logothetis, Diomedes E, Osman, Roman

“…Phosphoinositides like phosphatidylinositol 4,5-bisphosphate (PIP sub(2)) are negatively charged lipids that play a pivotal role in membrane trafficking,…”
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A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP^sub 2 by Lupyan, Dmitry, Mezei, Mihaly, Logothetis, Diomedes E, Osman, Roman

“…Phosphoinositides like phosphatidylinositol 4,5-bisphosphate (PIP2) are negatively charged lipids that play a pivotal role in membrane trafficking, signal…”
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A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP 2 by Lupyan, Dmitry, Mezei, Mihaly, Logothetis, Diomedes E., Osman, Roman

“…Phosphoinositides like phosphatidylinositol 4,5- bisphosphate (PIP 2) are negatively charged lipids that play a pivotal role in membrane trafficking, signal…”
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A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A 2A Adenosine Receptor by Lyman, Edward, Higgs, Chris, Kim, Byungchan, Lupyan, Dmitry, Shelley, John C., Farid, Ramy, Voth, Gregory A.

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