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There are 21488 results for: content related to: Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side-chain analogues

  1. Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests

    Journal of Computational Chemistry

    Volume 23, Issue 16, December 2002, Pages: 1515–1531, George A. Kaminski, Harry A. Stern, B. J. Berne, Richard A. Friesner, Yixiang X. Cao, Robert B. Murphy, Ruhong Zhou and Thomas A. Halgren

    Article first published online : 15 OCT 2002, DOI: 10.1002/jcc.10125

  2. Polarizable force fields for molecular dynamics simulations of biomolecules

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 5, Issue 2, March/April 2015, Pages: 241–254, Christopher M. Baker

    Article first published online : 26 JAN 2015, DOI: 10.1002/wcms.1215

  3. A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations

    Journal of Computational Chemistry

    Volume 24, Issue 3, February 2003, Pages: 267–276, George A. Kaminski, Richard A. Friesner and Ruhong Zhou

    Article first published online : 9 JAN 2003, DOI: 10.1002/jcc.10170

  4. A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics

    Journal of Computational Chemistry

    Volume 34, Issue 13, 15 May 2013, Pages: 1112–1124, Michel Masella, Daniel Borgis and Philippe Cuniasse

    Article first published online : 5 FEB 2013, DOI: 10.1002/jcc.23237

  5. Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ

    Journal of Computational Chemistry

    Volume 33, Issue 11, 30 April 2012, Pages: 1142–1151, Timothy H. Click, Sergei Y. Ponomarev and George A. Kaminski

    Article first published online : 27 FEB 2012, DOI: 10.1002/jcc.22944

  6. Further insights in the ability of classical nonadditive potentials to model actinide ion–water interactions

    Journal of Computational Chemistry

    Volume 34, Issue 9, 5 April 2013, Pages: 707–719, Florent Réal, Michael Trumm, Bernd Schimmelpfennig, Michel Masella and Valérie Vallet

    Article first published online : 12 DEC 2012, DOI: 10.1002/jcc.23184

  7. Polarizable protein packing

    Journal of Computational Chemistry

    Volume 32, Issue 7, May 2011, Pages: 1334–1344, Albert H. Ng and Christopher D. Snow

    Article first published online : 24 JAN 2011, DOI: 10.1002/jcc.21714

  8. Coupled-Cluster Interaction Energies for 200-Atom Host–Guest Systems

    ChemPhysChem

    Volume 15, Issue 15, October 20, 2014, Pages: 3270–3281, Milica Andrejić, Prof. Ulf Ryde, Prof. Ricardo A. Mata and Dr. Pär Söderhjelm

    Article first published online : 26 SEP 2014, DOI: 10.1002/cphc.201402379

  9. Integrated Modeling Program, Applied Chemical Theory (IMPACT)

    Journal of Computational Chemistry

    Volume 26, Issue 16, December 2005, Pages: 1752–1780, Jay L. Banks, Hege S. Beard, Yixiang Cao, Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Y. Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio and Ronald M. Levy

    Article first published online : 6 OCT 2005, DOI: 10.1002/jcc.20292

  10. On combining Thole's induced point dipole model with fixed charge distributions in molecular mechanics force fields

    Journal of Computational Chemistry

    Volume 36, Issue 10, April 15, 2015, Pages: 739–750, Hanne S. Antila and Emppu Salonen

    Article first published online : 5 MAR 2015, DOI: 10.1002/jcc.23850

  11. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform

    Journal of Computational Chemistry

    Xiangda Peng, Yuebin Zhang, Huiying Chu and Guohui Li

    Article first published online : 23 OCT 2015, DOI: 10.1002/jcc.24227

  12. Cation–π Interactions between a Free-Base Porphyrin and an Ionic Liquid: A Computational Study

    ChemPhysChem

    Volume 13, Issue 7, May 14, 2012, Pages: 1743–1747, Zhen Cao, Dr. Shu Li and Dr. Tianying Yan

    Article first published online : 17 JAN 2012, DOI: 10.1002/cphc.201100868

  13. Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

    Journal of Computational Chemistry

    Volume 34, Issue 3, 30 January 2013, Pages: 163–174, Yang Zhong and Sandeep Patel

    Article first published online : 29 OCT 2012, DOI: 10.1002/jcc.23109

  14. Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields

    Journal of Computational Chemistry

    Volume 36, Issue 25, September 30, 2015, Pages: 1874–1884, Marie Zgarbová, Andreana M. Rosnik, F. Javier Luque, Carles Curutchet and Petr Jurečka

    Article first published online : 30 JUL 2015, DOI: 10.1002/jcc.24012

  15. A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field

    Journal of Computational Chemistry

    Volume 35, Issue 21, August 5, 2014, Pages: 1577–1591, Mike Devereux, Nohad Gresh, Jean-Philip Piquemal and Markus Meuwly

    Article first published online : 25 JUN 2014, DOI: 10.1002/jcc.23661

  16. A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

    Journal of Computational Chemistry

    Volume 35, Issue 10, 15 April 2014, Pages: 789–801, Oliwia M. Szklarczyk, Stephan J. Bachmann and Wilfred F. van Gunsteren

    Article first published online : 19 FEB 2014, DOI: 10.1002/jcc.23551

  17. CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model

    Journal of Computational Chemistry

    Volume 25, Issue 12, September 2004, Pages: 1504–1514, Sandeep Patel, Alexander D. Mackerell Jr. and Charles L. Brooks III

    Article first published online : 15 JUN 2004, DOI: 10.1002/jcc.20077

  18. Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects

    Journal of Computational Chemistry

    Volume 32, Issue 12, September 2011, Pages: 2664–2678, Michel Masella, Daniel Borgis and Philippe Cuniasse

    Article first published online : 6 JUN 2011, DOI: 10.1002/jcc.21846

  19. Two Different Models to Predict Ionic-Liquid Diffraction Patterns: Fixed-Charge versus Polarizable Potentials

    ChemPhysChem

    Volume 16, Issue 1, January 12, 2015, Pages: 197–203, Dr. Marco Campetella, Dr. Lorenzo Gontrani, Dr. Francesca Leonelli, Prof. Dr. Luigi Bencivenni and Prof. Dr. Ruggero Caminiti

    Article first published online : 30 OCT 2014, DOI: 10.1002/cphc.201402577

  20. The effects of polymorphisms in the DGAT1, leptin and growth hormone receptor gene loci on body energy, blood metabolic and reproductive traits of Holstein cows

    Animal Genetics

    Volume 40, Issue 1, February 2009, Pages: 10–17, G. Oikonomou, K. Angelopoulou, G. Arsenos, D. Zygoyiannis and G. Banos

    Article first published online : 24 SEP 2008, DOI: 10.1111/j.1365-2052.2008.01789.x