Search Results - "Ross, Gregory A"

OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space by Lu, Chao, Wu, Chuanjie, Ghoreishi, Delaram, Chen, Wei, Wang, Lingle, Damm, Wolfgang, Ross, Gregory A, Dahlgren, Markus K, Russell, Ellery, Von Bargen, Christopher D, Abel, Robert, Friesner, Richard A, Harder, Edward D

“…We report on the development and validation of the OPLS4 force field. OPLS4 builds upon our previous work with OPLS3e to improve model accuracy on challenging…”
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Rapid and accurate prediction and scoring of water molecules in protein binding sites by Ross, Gregory A, Morris, Garrett M, Biggin, Philip C

“…Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to…”
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Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin by Sridhar, Akshay, Ross, Gregory A, Biggin, Philip C

“…Water is often found to mediate interactions between a ligand and a protein. It can play a significant role in orientating the ligand within a binding pocket…”
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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo by Gill, Samuel C, Lim, Nathan M, Grinaway, Patrick B, Rustenburg, Ariën S, Fass, Josh, Ross, Gregory A, Chodera, John D, Mobley, David L

“…Accurately predicting protein–ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding…”
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The maximal and current accuracy of rigorous protein-ligand binding free energy calculations by Ross, Gregory A., Lu, Chao, Scarabelli, Guido, Albanese, Steven K., Houang, Evelyne, Abel, Robert, Harder, Edward D., Wang, Lingle

“…Computational techniques can speed up the identification of hits and accelerate the development of candidate molecules for drug discovery. Among techniques for…”
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Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo by Ross, Gregory A, Bodnarchuk, Michael S, Essex, Jonathan W

“…Water molecules play integral roles in the formation of many protein–ligand complexes, and recent computational efforts have been focused on predicting the…”
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Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo by Ross, Gregory A, Russell, Ellery, Deng, Yuqing, Lu, Chao, Harder, Edward D, Abel, Robert, Wang, Lingle

“…The prediction of protein–ligand binding affinities using free energy perturbation (FEP) is becoming increasingly routine in structure-based drug discovery…”
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Biomolecular Simulations under Realistic Macroscopic Salt Conditions by Ross, Gregory A, Rustenburg, Ariën S, Grinaway, Patrick B, Fass, Josh, Chodera, John D

“…Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally…”
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Inhaled nitric oxide induced NOS inhibition and rebound pulmonary hypertension: a role for superoxide and peroxynitrite in the intact lamb by Oishi, Peter, Grobe, Albert, Benavidez, Eileen, Ovadia, Boaz, Harmon, Cynthia, Ross, Gregory A, Hendricks-Munoz, Karen, Xu, Jie, Black, Stephen M, Fineman, Jeffrey R

“…Previous in vivo studies indicate that inhaled nitric oxide (NO) decreases nitric oxide synthase (NOS) activity and that this decrease is associated with…”
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Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations by Bruce Macdonald, Hannah E, Cave-Ayland, Christopher, Ross, Gregory A, Essex, Jonathan W

“…Computational methods to calculate ligand binding affinities are increasing in popularity, due to improvements in simulation algorithms, computational…”
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Purpura fulminans caused by community-associated methicillin-resistant Staphylococcus aureus by Fitzgerald, Casimir J., MD, Pranikoff, Thomas V., MD, Ross, Gregory A., MD, Mou, Steven, MD, Givner, Laurence B., MD, Shetty, Avinash K., MD

“…Sepsis-induced purpura fulminans is a rare but life-threatening condition characterized by rapidly progressive hemorrhagic infarction of the skin due to dermal…”
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One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery by Ross, Gregory A, Morris, Garrett M, Biggin, Philip C

“…A major goal in computational chemistry has been to discover the set of rules that can accurately predict the binding affinity of any protein-drug complex,…”
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Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo by Ross, Gregory A, Bruce Macdonald, Hannah E, Cave-Ayland, Christopher, Cabedo Martinez, Ana I, Essex, Jonathan W

“…The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water…”
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An intra-aortic guide wire: what "knot" to do by Ootaki, Yoshio, Ross, Gregory A, Zeller, Kristen A

“…We report a rare complication of central venous catheter placement in a 5-month-old baby…”
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Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo by Aldeghi, Matteo, Ross, Gregory A., Bodkin, Michael J., Essex, Jonathan W., Knapp, Stefan, Biggin, Philip C.

“…Conserved water molecules are of interest in drug design, as displacement of such waters can lead to higher affinity ligands, and in some cases, contribute…”
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Oseltamivir‐resistant 2009 H1N1 influenza pneumonia during therapy in a renal transplant recipient by Shetty, Avinash K., Ross, Gregory A., Pranikoff, Thomas, Gubareva, Larissa V., Sechrist, Catherine, Guirand, Derek M., Abramson, Jon, Lin, Jen‐Jar

“…Shetty AK, Ross GA, Pranikoff T, Gubareva LV, Sechrist C, Guirand DM, Abramson J, Lin J‐J. Oseltamivir‐resistant 2009 H1N1 influenza pneumonia during therapy…”
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Emergence of smooth muscle cell endothelin B-mediated vasoconstriction in lambs with experimental congenital heart disease and increased pulmonary blood flow by BLACK, Stephen M, MATA-GREENWOOD, Eugenia, ROSS, Gregory A, BEKKER, Janine M, JOHENGEN, Michael J, FINEMAN, Jeffrey R, DETTMAN, Robert W, OVADIA, Boaz, FITZGERALD, Robert K, REINHARTZ, Olaf, THELITZ, Stefan, STEINHORN, Robin H, GERRETS, Rene, HENDRICKS-MUNOZ, Karen

“…Endothelin-1 (ET-1) has been implicated in the pathophysiology of pulmonary hypertension. In 1-month-old lambs with increased pulmonary blood flow, we have…”
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Endothelial alterations during inhaled NO in lambs with pulmonary hypertension: implications for rebound hypertension by Ross, Gregory A, Oishi, Peter, Azakie, Anthony, Fratz, Sohrab, Fitzgerald, Robert K, Johengen, Michael J, Harmon, Cynthia, Hendricks-Munoz, Karen, Xu, Jie, Black, Stephen M, Fineman, Jeffrey R

“…Clinically significant increases in pulmonary vascular resistance (PVR) have been noted upon acute withdrawal of inhaled nitric oxide (iNO). Previous studies…”
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Tezosentan, a combined parenteral endothelin receptor antagonist, produces pulmonary vasodilation in lambs with acute and chronic pulmonary hypertension by Fitzgerald, Robert K, Oishi, Peter, Ovadia, Boaz, Ross, Gregory A, Reinhartz, Olaf, Johengen, Michael J, Fineman, Jeffrey R

“…To investigate the hemodynamic effects of tezosentan in the intact lamb both at rest and during acute and chronic pulmonary hypertension. Prospective,…”
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Pediatric Critical Care, 3rd ed by Ross, Gregory A.

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