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There are 13721 results for: content related to: Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

  1. Combination of the CHARMM27 force field with united-atom lipid force fields

    Journal of Computational Chemistry

    Volume 32, Issue 7, May 2011, Pages: 1400–1410, Nicolas Sapay and D. Peter Tieleman

    Article first published online : 31 DEC 2010, DOI: 10.1002/jcc.21726

  2. CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

    Journal of Computational Chemistry

    Volume 28, Issue 2, 30 January 2007, Pages: 495–507, Evelyn Mayaan, Adam Moser, Alexander D. MacKerell Jr and Darrin M. York

    Article first published online : 21 DEC 2006, DOI: 10.1002/jcc.20474

  3. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

    Journal of Computational Chemistry

    Volume 21, Issue 2, 30 January 2000, Pages: 86–104, Nicolas Foloppe and Alexander D. MacKerell, Jr.

    Article first published online : 4 JAN 2000, DOI: 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G

  4. CHARMM: The biomolecular simulation program

    Journal of Computational Chemistry

    Volume 30, Issue 10, 30 July 2009, Pages: 1545–1614, B. R. Brooks, C. L. Brooks III, A. D. Mackerell Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York and M. Karplus

    Article first published online : 14 MAY 2009, DOI: 10.1002/jcc.21287

  5. Empirical force fields for biological macromolecules: Overview and issues

    Journal of Computational Chemistry

    Volume 25, Issue 13, October 2004, Pages: 1584–1604, Alexander D. Mackerell Jr.

    Article first published online : 1 JUL 2004, DOI: 10.1002/jcc.20082

  6. Modification of the CHARMM force field for DMPC lipid bilayer

    Journal of Computational Chemistry

    Volume 29, Issue 14, 15 November 2008, Pages: 2359–2369, Carl-Johan Högberg, Alexei M. Nikitin and Alexander P. Lyubartsev

    Article first published online : 29 MAY 2008, DOI: 10.1002/jcc.20974

  7. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

    Journal of Computational Chemistry

    Volume 21, Issue 2, 30 January 2000, Pages: 105–120, Alexander D. MacKerell Jr. and Nilesh K. Banavali

    Article first published online : 4 JAN 2000, DOI: 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P

  8. Classical force field parameters for the heme prosthetic group of cytochrome c

    Journal of Computational Chemistry

    Volume 25, Issue 13, October 2004, Pages: 1613–1622, Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry and Zaida Luthey-Schulten

    Article first published online : 2 JUL 2004, DOI: 10.1002/jcc.20079

  9. Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers

    Journal of Computational Chemistry

    Volume 31, Issue 2, 30 January 2010, Pages: 266–277, Priyanka Prakash and Ramasubbu Sankararamakrishnan

    Article first published online : 27 MAY 2009, DOI: 10.1002/jcc.21313

  10. Symmetrization of the AMBER and CHARMM force fields

    Journal of Computational Chemistry

    Volume 31, Issue 7, May 2010, Pages: 1402–1409, Edyta Małolepsza, Birgit Strodel, Mey Khalili, Semen Trygubenko, Szilard N. Fejer and David J. Wales

    Article first published online : 15 JAN 2010, DOI: 10.1002/jcc.21425

    Corrected by:

    Erratum: Erratum: Symmetrization of the AMBER and CHARMM force fields [J. Comp. Chem. 31, 1402]

    Vol. 33, Issue 27, 2209, Article first published online: 27 JUL 2012

  11. CH/π interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field

    Journal of Computational Chemistry

    Volume 26, Issue 14, 15 November 2005, Pages: 1452–1463, Alba T. Macias and Alexander D. MacKerell Jr.

    Article first published online : 8 AUG 2005, DOI: 10.1002/jcc.20281

  12. Molecular mechanics models for tetracycline analogs

    Journal of Computational Chemistry

    Volume 30, Issue 2, 30 January 2009, Pages: 243–255, Alexey Aleksandrov and Thomas Simonson

    Article first published online : 9 JUL 2008, DOI: 10.1002/jcc.21040

  13. SwissParam: A fast force field generation tool for small organic molecules

    Journal of Computational Chemistry

    Volume 32, Issue 11, August 2011, Pages: 2359–2368, Vincent Zoete, Michel A. Cuendet, Aurélien Grosdidier and Olivier Michielin

    Article first published online : 3 MAY 2011, DOI: 10.1002/jcc.21816

  14. Establishing effective simulation protocols for β- and α/β-peptides. III. Molecular mechanical model for acyclic β-amino acids

    Journal of Computational Chemistry

    Volume 31, Issue 10, 30 July 2010, Pages: 2063–2077, Xiao Zhu, Peter Koenig, Michael Hoffmann, Arun Yethiraj and Qiang Cui

    Article first published online : 19 FEB 2010, DOI: 10.1002/jcc.21493

  15. Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions

    Journal of Computational Chemistry

    Volume 32, Issue 7, May 2011, Pages: 1431–1440, Allyn R. Brice and Brian N. Dominy

    Article first published online : 1 FEB 2011, DOI: 10.1002/jcc.21727

  16. Investigation on the individual contributions of N[BOND]H···O[DOUBLE BOND]C and C[BOND]H···O[DOUBLE BOND]C interactions to the binding energies of β-sheet models

    Journal of Computational Chemistry

    Volume 31, Issue 5, 15 April 2010, Pages: 1036–1044, Chang-Sheng Wang and Chang-Liang Sun

    Article first published online : 9 OCT 2009, DOI: 10.1002/jcc.21390

  17. Charge optimization of the interface between protein kinases and their ligands

    Journal of Computational Chemistry

    Volume 25, Issue 11, August 2004, Pages: 1416–1429, Peter A. Sims, Chung F. Wong and J. Andrew McCammon

    Article first published online : 2 JUN 2004, DOI: 10.1002/jcc.20067

  18. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

    Journal of Computational Chemistry

    Volume 25, Issue 11, August 2004, Pages: 1400–1415, Alexander D. Mackerell Jr., Michael Feig and Charles L. Brooks III

    Article first published online : 2 JUN 2004, DOI: 10.1002/jcc.20065

  19. A molecular mechanics model for imatinib and imatinib:kinase binding

    Journal of Computational Chemistry

    Volume 31, Issue 7, May 2010, Pages: 1550–1560, Alexey Aleksandrov and Thomas Simonson

    Article first published online : 17 DEC 2009, DOI: 10.1002/jcc.21442

  20. A molecular mechanics force field for biologically important sterols

    Journal of Computational Chemistry

    Volume 26, Issue 13, October 2005, Pages: 1383–1399, Zoe Cournia, Jeremy C. Smith and G. Matthias Ullmann

    Article first published online : 18 JUL 2005, DOI: 10.1002/jcc.20277