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There are 3025 results for: content related to: Comparison of multiple Amber force fields and development of improved protein backbone parameters

  1. You have free access to this content
    Force field influences in β-hairpin folding simulations

    Protein Science

    Volume 15, Issue 11, November 2006, Pages: 2642–2655, Thu Zar Lwin and Ray Luo

    Article first published online : 1 JAN 2009, DOI: 10.1110/ps.062438006

  2. Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

    International Journal of Quantum Chemistry

    Volume 110, Issue 15, December 2010, Pages: 2865–2879, Mahmoud Moradi, Jung-Goo Lee, Volodymyr Babin, Christopher Roland and Celeste Sagui

    Article first published online : 24 AUG 2010, DOI: 10.1002/qua.22875

  3. Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins

    Journal of Computational Chemistry

    Volume 24, Issue 1, 15 January 2003, Pages: 21–31, Asim Okur, Bentley Strockbine, Viktor Hornak and Carlos Simmerling

    Article first published online : 25 NOV 2002, DOI: 10.1002/jcc.10184

  4. New Force Field on Modeling Intrinsically Disordered Proteins

    Chemical Biology & Drug Design

    Volume 84, Issue 3, September 2014, Pages: 253–269, Wei Wang, Wei Ye, Cheng Jiang, Ray Luo and Hai-Feng Chen

    Article first published online : 1 JUL 2014, DOI: 10.1111/cbdd.12314

  5. Force field parameters for rotation around χ torsion axis in nucleic acids

    Journal of Computational Chemistry

    Volume 29, Issue 15, 30 November 2008, Pages: 2531–2542, Hirotaka Ode, Yuri Matsuo, Saburo Neya and Tyuji Hoshino

    Article first published online : 12 MAY 2008, DOI: 10.1002/jcc.21006

  6. Molecular dynamics (MD) simulations of VIP and PACAP27

    Biopolymers

    Volume 91, Issue 5, May 2009, Pages: 391–400, Francesc J. Corcho, Paul Mokoena, Krishna Bisetty and Juan J. Perez

    Article first published online : 20 JAN 2009, DOI: 10.1002/bip.21147

  7. Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations

    Biopolymers

    Volume 101, Issue 10, October 2014, Pages: 985–991, Indrajit Deb, Joanna Sarzynska, Lennart Nilsson and Ansuman Lahiri

    Article first published online : 23 JUL 2014, DOI: 10.1002/bip.22495

  8. Accelerated molecular dynamics simulations of protein folding

    Journal of Computational Chemistry

    Volume 36, Issue 20, July 30, 2015, Pages: 1536–1549, Yinglong Miao, Ferran Feixas, Changsun Eun and J. Andrew McCammon

    Article first published online : 12 JUN 2015, DOI: 10.1002/jcc.23964

  9. Molecular mechanics parameters for the FapydG DNA lesion

    Journal of Computational Chemistry

    Volume 29, Issue 1, 15 January 2008, Pages: 17–23, Kun Song, Viktor Hornak, Carlos De Los Santos, Arthur P. Grollman and Carlos Simmerling

    Article first published online : 5 JUN 2007, DOI: 10.1002/jcc.20625

  10. Origin of intrinsic 310-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field

    Journal of Computational Chemistry

    Volume 28, Issue 10, 30 July 2007, Pages: 1648–1657, Anna Jagielska and Jeffrey Skolnick

    Article first published online : 6 MAR 2007, DOI: 10.1002/jcc.20616

  11. Deciphering the Selectivity of Bombyx mori Pheromone Binding Protein for Bombykol over Bombykal: A Theoretical Approach

    ChemPhysChem

    Volume 9, Issue 18, December 22, 2008, Pages: 2785–2793, Landry Charlier, Serge Antonczak, Emmanuelle Jacquin-Joly, Daniel Cabrol-Bass and Jérôme Golebiowski

    Article first published online : 21 NOV 2008, DOI: 10.1002/cphc.200800343

  12. Molecular dynamics simulations of polarizable DNA in crystal environment

    International Journal of Quantum Chemistry

    Volume 106, Issue 15, 2006, Pages: 3260–3269, Volodymyr Babin, Jason Baucom, Thomas A. Darden and Celeste Sagui

    Article first published online : 1 AUG 2006, DOI: 10.1002/qua.21152

  13. Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation

    Journal of Computational Chemistry

    Volume 29, Issue 12, September 2008, Pages: 1930–1944, Daisuke Katagiri, Hideyoshi Fuji, Saburo Neya and Tyuji Hoshino

    Article first published online : 25 MAR 2008, DOI: 10.1002/jcc.20963

  14. Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

    Proteins: Structure, Function, and Bioinformatics

    Volume 71, Issue 2, 1 May 2008, Pages: 684–694, Nikola Trbovic, Byungchan Kim, Richard A. Friesner and Arthur G. Palmer III

    Article first published online : 1 NOV 2007, DOI: 10.1002/prot.21750

  15. You have free access to this content
    Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 8, June 2010, Pages: 1889–1899, Ryan Day, Dietmar Paschek and Angel E. Garcia

    Article first published online : 16 FEB 2010, DOI: 10.1002/prot.22702

  16. Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

    Proteins: Structure, Function, and Bioinformatics

    Volume 79, Issue 4, April 2011, Pages: 1318–1328, Robert B. Best and Jeetain Mittal

    Article first published online : 14 FEB 2011, DOI: 10.1002/prot.22972

  17. Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils

    Proteins: Structure, Function, and Bioinformatics

    Volume 74, Issue 3, 15 February 2009, Pages: 612–629, Scott S. Pendley, Yihua B. Yu and Thomas E. Cheatham III

    Article first published online : 14 AUG 2008, DOI: 10.1002/prot.22177

  18. Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics

    Proteins: Structure, Function, and Bioinformatics

    Volume 83, Issue 9, September 2015, Pages: 1665–1676, George A. Pantelopulos, Sudipto Mukherjee and Vincent A. Voelz

    Article first published online : 21 JUL 2015, DOI: 10.1002/prot.24852

  19. You have full text access to this OnlineOpen article
    Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 11, 15 August 2010, Pages: 2523–2532, Morgan Lawrenz, Jeff Wereszczynski, Rommie Amaro, Ross Walker, Adrian Roitberg and J. Andrew McCammon

    Article first published online : 3 MAY 2010, DOI: 10.1002/prot.22761

  20. NMR-Based Protein Potentials

    Angewandte Chemie

    Volume 122, Issue 38, September 10, 2010, Pages: 6930–6932, Dr. Da-Wei Li and Prof. Rafael Brüschweiler

    Article first published online : 16 AUG 2010, DOI: 10.1002/ange.201001898