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1
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Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

Mobley, David L ; Bayly, Christopher I ; Cooper, Matthew D ; Shirts, Michael R ; Dill, Ken A

Journal of chemical theory and computation, 10 March 2015, Vol.11(3), pp.1347 [Peer Reviewed Journal]

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Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

Beauchamp, Kyle A ; Behr, Julie M ; Rustenburg, Ariën S ; Bayly, Christopher I ; Kroenlein, Kenneth ; Chodera, John D

The journal of physical chemistry. B, 08 October 2015, Vol.119(40), pp.12912-20 [Peer Reviewed Journal]

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3
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Peter A. Kollman, 1945–2001

Bayly, Christopher I

Biophysical Journal, 2001, Vol.81(4), pp.2422-2422 [Peer Reviewed Journal]

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4
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Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations

Wall, Michael E ; Calabró, Gaetano ; Bayly, Christopher I ; Mobley, David L ; Warren, Gregory L

Journal of the American Chemical Society, 20 March 2019, Vol.141(11), pp.4711-4720 [Peer Reviewed Journal]

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5
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Predictions of hydration free energies from all-atom molecular dynamics simulations

Mobley, David L ; Bayly, Christopher I ; Cooper, Matthew D ; Dill, Ken A

The journal of physical chemistry. B, 09 April 2009, Vol.113(14), pp.4533-7 [Peer Reviewed Journal]

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6
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The BLUES Report: Towards fragment binding mode occupancies

Mobley, David L ; Lim, Natham M ; Gill, Samuel L ; Bayly, Christopher I ; Warren, Gregory

2018

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7
An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis
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An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis

Wang, Wei ; Lim, Wendell A. ; Jakalian, Araz ; Wang, Jian ; Wang, Junmei ; Luo, Ray ; Bayly, Christopher I. ; Kollman, Peter A.

Journal of the American Chemical Society, 05/2001, Vol.123(17), pp.3986-3994 [Peer Reviewed Journal]

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8
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Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions

Truchon, Jean‐François ; Nicholl' S, Anthony ; Grant, J. Andrew ; Iftimie, Radu I. ; Roux, Benoît ; Bayly, Christopher I.

Journal of Computational Chemistry, March 2010, Vol.31(4), pp.811-824 [Peer Reviewed Journal]

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9
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Predicting small-molecule solvation free energies: an informal blind test for computational chemistry

Nicholls, Anthony ; Mobley, David L ; Guthrie, J Peter ; Chodera, John D ; Bayly, Christopher I ; Cooper, Matthew D ; Pande, Vijay S

Journal of medicinal chemistry, 28 February 2008, Vol.51(4), pp.769-79 [Peer Reviewed Journal]

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10
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Escaping Atom Types in Force Fields Using Direct Chemical Perception

Mobley, David L ; Bannan, Caitlin C ; Rizzi, Andrea ; Bayly, Christopher I ; Chodera, John D ; Lim, Victoria T ; Lim, Nathan M ; Beauchamp, Kyle A ; Slochower, David R ; Shirts, Michael R ; Gilson, Michael K ; Eastman, Peter K

Journal of chemical theory and computation, 13 November 2018, Vol.14(11), pp.6076-6092 [Peer Reviewed Journal]

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11
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J . Am . Chem . Soc . 1995 , 117 , 5179−5197
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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J . Am . Chem . Soc . 1995 , 117 , 5179−5197

Cornell, Wendy D. ; Cieplak, Piotr ; Bayly, Christopher I. ; Gould, Ian R. ; Merz, Kenneth M. ; Ferguson, David M. ; Spellmeyer, David C. ; Fox, Thomas ; Caldwell, James W. ; Kollman, Peter A.

Journal of the American Chemical Society, 01/1996, Vol.118(9), pp.2309-2309 [Peer Reviewed Journal]

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12
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Corrigendum to “Design and synthesis of dipeptidyl nitriles as potent, selective, and reversible inhibitors of cathepsin C” [Bioorg. Med. Chem. Lett. 19 (2009) 5392]

Guay, Daniel ; Beaulieu, Christian ; Truchon, Jean-Francois ; Reddy, T. Jagadeeswar ; Bayly, Christopher I ; Zamboni, Robert ; Methot, Nathalie ; Rubin, Joel ; Ethier, Diane ; Percival, M. David

Bioorganic & Medicinal Chemistry Letters, 2010, Vol.20(4), pp.1463-1463 [Peer Reviewed Journal]

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13
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Solid phase parallel synthesis of highly substituted thiophene derivatives and identification of novel phosphodiesterase-4 (PDE-4) inhibitors

Han, Yongxin ; Giroux, André ; Lépine, Carole ; Laliberté, France ; Huang, Zheng ; Perrier, Hélène ; Bayly, Christopher I ; Young, Robert N

Tetrahedron, 1999, Vol.55(39), pp.11669-11685 [Peer Reviewed Journal]

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14
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Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem

Truchon, Jean-François ; Bayly, Christopher I

Journal of chemical information and modeling, 2007, Vol.47(2), pp.488-508 [Peer Reviewed Journal]

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15
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GLARE: a new approach for filtering large reagent lists in combinatorial library design using product properties

Truchon, Jean-François ; Bayly, Christopher I

Journal of chemical information and modeling, 2006, Vol.46(4), pp.1536-48 [Peer Reviewed Journal]

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16
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Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation

Jakalian, Araz ; Jack, David B. ; Bayly, Christopher I. Frenking, Gernot ; Jorgensen, William L.

Journal of Computational Chemistry, December 2002, Vol.23(16), pp.1623-1641 [Peer Reviewed Journal]

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17
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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

Jakalian, Araz ; Jack, David B ; Bayly, Christopher I

Journal of computational chemistry, December 2002, Vol.23(16), pp.1623-41 [Peer Reviewed Journal]

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18
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Identification of a nonbasic, nitrile-containing cathepsin K inhibitor (MK-1256) that is efficacious in a monkey model of osteoporosis

Robichaud, Jöel ; Black, W Cameron ; Thérien, Michel ; Paquet, Julie ; Oballa, Renata M ; Bayly, Christopher I ; Mckay, Daniel J ; Wang, Qingping ; Isabel, Elise ; Léger, Serge ; Mellon, Christophe ; Kimmel, Donald B ; Wesolowski, Gregg ; Percival, M David ; Massé, Fréderic

Journal of medicinal chemistry, 23 October 2008, Vol.51(20), pp.6410-20 [Peer Reviewed Journal]

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19
β-Substituted Cyclohexanecarboxamide:  A Nonpeptidic Framework for the Design of Potent Inhibitors of Cathepsin K
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β-Substituted Cyclohexanecarboxamide:  A Nonpeptidic Framework for the Design of Potent Inhibitors of Cathepsin K

Crane, Sheldon N. ; Black, W. Cameron ; Palmer, James T. ; Davis, Dana E. ; Setti, Eduardo ; Robichaud, Joel ; Paquet, Julie ; Oballa, Renata M. ; Bayly, Christopher I. ; Mckay, Daniel J. ; Somoza, John R. ; Chauret, Natalie ; Seto, Carmai ; Scheigetz, John ; Wesolowski, Greg ; Massé, Frederic ; Desmarais, Sylvie ; Ouellet, Marc

Journal of Medicinal Chemistry, 02/2006, Vol.49(3), pp.1066-1079 [Peer Reviewed Journal]

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20
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Beta-substituted cyclohexanecarboxamide: a nonpeptidic framework for the design of potent inhibitors of cathepsin K

Crane, Sheldon N ; Black, W Cameron ; Palmer, James T ; Davis, Dana E ; Setti, Eduardo ; Robichaud, Joel ; Paquet, Julie ; Oballa, Renata M ; Bayly, Christopher I ; Mckay, Daniel J ; Somoza, John R ; Chauret, Natalie ; Seto, Carmai ; Scheigetz, John ; Wesolowski, Greg ; Massé, Frederic ; Desmarais, Sylvie ; Ouellet, Marc

Journal of medicinal chemistry, 09 February 2006, Vol.49(3), pp.1066-79 [Peer Reviewed Journal]

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21
Material Type:
Research Dataset
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Supporting Information: Toward learned chemical perception of force field typing rules

Zanette, Camila ; Bannan, Caitlin C. ; Bayly, Christopher I. ; Fass, Josh ; Gilson, Michael K. ; Shirts, Michael R. ; Chodera, John D. ; Mobley, David L.

2018

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22
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CCDC 1417025: Experimental Crystal Structure Determination

McGaughey, Georgia ; Bayly, Christopher I. ; Cox, Christopher D. ; Schreier, John D. ; Breslin, Michael J. ; Bogusky, Michael ; Pitzenberger, Steve ; Ball, Richard ; Coleman, Paul J.

2015

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23
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CCDC 1417026: Experimental Crystal Structure Determination

McGaughey, Georgia ; Bayly, Christopher I. ; Cox, Christopher D. ; Schreier, John D. ; Breslin, Michael J. ; Bogusky, Michael ; Pitzenberger, Steve ; Ball, Richard ; Coleman, Paul J.

2015

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24
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Solid phase synthesis of selective caspase-3 peptide inhibitors

Grimm, Erich L ; Roy, Bruno ; Aspiotis, Renee ; Bayly, Christopher I ; Nicholson, Donald W ; Rasper, Dita M ; Renaud, Johanne ; Roy, Sophie ; Tam, John ; Tawa, Paul ; Vaillancourt, John P ; Xanthoudakis, Steven ; Zamboni, Robert J

Bioorganic & Medicinal Chemistry, 01 March 2004, Vol.12(5), pp.845-851 [Peer Reviewed Journal]

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25
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Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

Mobley, David L ; Bayly, Christopher I ; Cooper, Matthew D ; Shirts, Michael R ; Dill, Ken A

Journal of chemical theory and computation, 10 February 2009, Vol.5(2), pp.350-358 [Peer Reviewed Journal]

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26
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Integrated Continuum Dielectric Approaches to treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation

Truchon, Jean-François ; Nicholls, Anthony ; Roux, Benoît ; Iftimie, Radu I ; Bayly, Christopher I

Journal of chemical theory and computation, 14 July 2009, Vol.5(7), pp.1785-1802 [Peer Reviewed Journal]

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27
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Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid

Lim, Victoria T ; Bayly, Christopher I ; Fusti-Molnar, Laszlo ; Mobley, David L

Journal of chemical information and modeling, 28 May 2019, Vol.59(5), pp.1957-1964 [Peer Reviewed Journal]

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28
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Accurate Molecular Polarizabilities Based on Continuum Electrostatics

Truchon, Jean-François ; Nicholls, Anthony ; Iftimie, Radu I ; Roux, Benoît ; Bayly, Christopher I

Journal of chemical theory and computation, 09 September 2008, Vol.4(9), pp.1480-1493 [Peer Reviewed Journal]

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29
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Consensus bond‐charge increments fitted to electrostatic potential or field of many compounds: Application to MMFF94 training set

Bush, Bruce L. ; Bayly, Christopher I. ; Halgren, Thomas A.

Journal of Computational Chemistry, 15 November 1999, Vol.20(14), pp.1495-1516 [Peer Reviewed Journal]

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30
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A generally applicable method for assessing the electrophilicity and reactivity of diverse nitrile-containing compounds

Oballa, Renata M ; Truchon, Jean-François ; Bayly, Christopher I ; Chauret, Nathalie ; Day, Stephen ; Crane, Sheldon ; Berthelette, Carl

Bioorganic & Medicinal Chemistry Letters, 2007, Vol.17(4), pp.998-1002 [Peer Reviewed Journal]

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31
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Design and synthesis of dipeptidyl nitriles as potent, selective, and reversible inhibitors of cathepsin C

Guay, Daniel ; Beaulieu, Christian ; Truchon, Jean-Francois ; Jagadeeswar Reddy, T ; Zamboni, Robert ; Bayly, Christopher I ; Methot, Nathalie ; Rubin, Joel ; Ethier, Diane ; David Percival, M

Bioorganic & medicinal chemistry letters, 15 September 2009, Vol.19(18), pp.5392-6 [Peer Reviewed Journal]

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32
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Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method

Jakalian, Araz ; Bush, Bruce L. ; Jack, David B. ; Bayly, Christopher I.

Journal of Computational Chemistry, 30 January 2000, Vol.21(2), pp.132-146 [Peer Reviewed Journal]

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33
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Structure-based design of COX-2 selectivity into flurbiprofen

Bayly, Christopher I ; Black, W.Cameron ; Léger, Serge ; Ouimet, Nathalie ; Ouellet, Marc ; Percival, M.David

Bioorganic & Medicinal Chemistry Letters, 1999, Vol.9(3), pp.307-312 [Peer Reviewed Journal]

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34
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Primary amides as selective inhibitors of cathepsin K

Léger, Serge ; Bayly, Christopher I ; Black, W. Cameron ; Desmarais, Sylvie ; Falgueyret, Jean-Pierre ; Massé, Frédéric ; Percival, M. David ; Truchon, Jean-François

Bioorganic & Medicinal Chemistry Letters, 2007, Vol.17(15), pp.4328-4332 [Peer Reviewed Journal]

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35
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Toward Learned Chemical Perception of Force Field Typing Rules

Zanette, Camila ; Bannan, Caitlin C ; Bayly, Christopher I ; Fass, Josh ; Gilson, Michael K ; Shirts, Michael R ; Chodera, John D ; Mobley, David L

Journal of chemical theory and computation, 08 January 2019, Vol.15(1), pp.402-423 [Peer Reviewed Journal]

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36
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Discovery of [(3-bromo-7-cyano-2-naphthyl)(difluoro)methyl]phosphonic acid, a potent and orally active small molecule PTP1B inhibitor

Han, Yongxin ; Belley, Michel ; Bayly, Christopher I ; Colucci, John ; Dufresne, Claude ; Giroux, Andre ; Lau, Cheuk K ; Leblanc, Yves ; Mckay, Daniel ; Therien, Michel ; Wilson, Marie-Claire ; Skorey, Kathryn ; Chan, Chi-Chung ; Scapin, Giovana ; Kennedy, Brian P

Bioorganic & Medicinal Chemistry Letters, 2008, Vol.18(11), pp.3200-3205 [Peer Reviewed Journal]

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37
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Comparison of topological, shape, and docking methods in virtual screening

Mcgaughey, Georgia B ; Sheridan, Robert P ; Bayly, Christopher I ; Culberson, J Chris ; Kreatsoulas, Constantine ; Lindsley, Stacey ; Maiorov, Vladimir ; Truchon, Jean-Francois ; Cornell, Wendy D

Journal of chemical information and modeling, 2007, Vol.47(4), pp.1504-19 [Peer Reviewed Journal]

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38
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Beta-substituted cyclohexanecarboxamide cathepsin K inhibitors: modification of the 1,2-disubstituted aromatic core

Robichaud, Joël ; Bayly, Christopher I ; Black, W Cameron ; Desmarais, Sylvie ; Léger, Serge ; Massé, Frédéric ; Mckay, Daniel J ; Oballa, Renata M ; Pâquet, Julie ; Percival, M David ; Truchon, Jean-François ; Wesolowski, Gregg ; Crane

Bioorganic & medicinal chemistry letters, 01 June 2007, Vol.17(11), pp.3146-51 [Peer Reviewed Journal]

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