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There are 2149 results for: content related to: Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

  1. 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

    Version of Record online : 1 JUL 2014, DOI: 10.1111/cbdd.12314

  2. Reparameterizations of the χ Torsion and Lennard-Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines

    Journal of Computational Chemistry

    Volume 37, Issue 17, June 30, 2016, Pages: 1576–1588, Indrajit Deb, Rupak Pal, Joanna Sarzynska and Ansuman Lahiri

    Version of Record online : 30 MAR 2016, DOI: 10.1002/jcc.24374

  3. 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

    Version of Record online : 20 JAN 2009, DOI: 10.1002/bip.21147

  4. 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

    Version of Record online : 12 MAY 2008, DOI: 10.1002/jcc.21006

  5. Comparison of multiple Amber force fields and development of improved protein backbone parameters

    Proteins: Structure, Function, and Bioinformatics

    Volume 65, Issue 3, 15 November 2006, Pages: 712–725, Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg and Carlos Simmerling

    Version of Record online : 15 SEP 2006, DOI: 10.1002/prot.21123

  6. 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

    Version of Record online : 1 JAN 2009, DOI: 10.1110/ps.062438006

  7. 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

    Version of Record online : 24 AUG 2010, DOI: 10.1002/qua.22875

  8. 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

    Version of Record online : 25 NOV 2002, DOI: 10.1002/jcc.10184

  9. 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

    Version of Record online : 1 NOV 2007, DOI: 10.1002/prot.21750

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    Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

    Protein Science

    Volume 25, Issue 1, January 2016, Pages: 87–102, Pawel A. Janowski, Chunmei Liu, Jason Deckman and David A. Case

    Version of Record online : 11 JUN 2015, DOI: 10.1002/pro.2713

  11. You have full text access to this OnlineOpen article
    Improved side-chain torsion potentials for the Amber ff99SB protein force field

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 8, June 2010, Pages: 1950–1958, Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L. Klepeis, Ron O. Dror and David E. Shaw

    Version of Record online : 9 MAR 2010, DOI: 10.1002/prot.22711

  12. 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

    Version of Record online : 23 JUL 2014, DOI: 10.1002/bip.22495

  13. 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

    Version of Record online : 3 MAY 2010, DOI: 10.1002/prot.22761

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    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

    Version of Record online : 16 FEB 2010, DOI: 10.1002/prot.22702

  15. NMR-Based Protein Potentials

    Angewandte Chemie

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

    Version of Record online : 16 AUG 2010, DOI: 10.1002/ange.201001898

  16. NMR-Based Protein Potentials

    Angewandte Chemie International Edition

    Volume 49, Issue 38, September 10, 2010, Pages: 6778–6780, Dr. Da-Wei Li and Prof. Rafael Brüschweiler

    Version of Record online : 16 AUG 2010, DOI: 10.1002/anie.201001898

  17. 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

    Version of Record online : 5 JUN 2007, DOI: 10.1002/jcc.20625

  18. Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations

    Journal of Computational Chemistry

    Volume 37, Issue 19, July 15, 2016, Pages: 1828–1838, Andreas Köster, Thomas Spura, Gábor Rutkai, Jan Kessler, Hendrik Wiebeler, Jadran Vrabec and Thomas D. Kühne

    Version of Record online : 27 MAY 2016, DOI: 10.1002/jcc.24398

  19. Calibration of forcefields for molecular simulation: Sequential design of computer experiments for building cost-efficient kriging metamodels

    Journal of Computational Chemistry

    Volume 35, Issue 2, 15 January 2014, Pages: 130–149, Fabien Cailliez, Arnaud Bourasseau and Pascal Pernot

    Version of Record online : 25 OCT 2013, DOI: 10.1002/jcc.23475

  20. A hybrid QM/MM method employing real space grids for QM water in the TIP4P water solvents

    Journal of Computational Chemistry

    Volume 22, Issue 12, September 2001, Pages: 1252–1261, H. Takahashi, T. Hori, H. Hashimoto and T. Nitta

    Version of Record online : 28 JUN 2001, DOI: 10.1002/jcc.1082