Search Results

There are 7505116 results for: content related to: Adaptation of a fast Fourier transform-based docking algorithm for protein design

  1. Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking

    Proteins: Structure, Function, and Bioinformatics

    Volume 66, Issue 2, 1 February 2007, Pages: 399–421, Sheng-You Huang and Xiaoqin Zou

    Version of Record online : 9 NOV 2006, DOI: 10.1002/prot.21214

  2. EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization

    Proteins: Structure, Function, and Bioinformatics

    Volume 67, Issue 4, June 2007, Pages: 1010–1025, Aurélien Grosdidier, Vincent Zoete and Olivier Michielin

    Version of Record online : 22 MAR 2007, DOI: 10.1002/prot.21367

  3. PRL-dock: Protein-ligand docking based on hydrogen bond matching and probabilistic relaxation labeling

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 9, August 2012, Pages: 2137–2153, Meng-Yun Wu, Dao-Qing Dai and Hong Yan

    Version of Record online : 4 JUN 2012, DOI: 10.1002/prot.24104

  4. FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

    Journal of Computational Chemistry

    Volume 34, Issue 1, 5 January 2013, Pages: 67–75, Yu Liu, Lei Zhao, Wentao Li, Dongyu Zhao, Miao Song and Yongliang Yang

    Version of Record online : 7 SEP 2012, DOI: 10.1002/jcc.23108

  5. Principles of docking: An overview of search algorithms and a guide to scoring functions

    Proteins: Structure, Function, and Bioinformatics

    Volume 47, Issue 4, 1 June 2002, Pages: 409–443, Inbal Halperin, Buyong Ma, Haim Wolfson and Ruth Nussinov

    Version of Record online : 9 APR 2002, DOI: 10.1002/prot.10115

  6. Protein–protein docking dealing with the unknown

    Journal of Computational Chemistry

    Volume 31, Issue 2, 30 January 2010, Pages: 317–342, Irina S. Moreira, Pedro A. Fernandes and Maria J. Ramos

    Version of Record online : 21 MAY 2009, DOI: 10.1002/jcc.21276

  7. Accounting for loop flexibility during protein–protein docking

    Proteins: Structure, Function, and Bioinformatics

    Volume 62, Issue 4, 1 March 2006, Pages: 956–969, Karine Bastard, Chantal Prévost and Martin Zacharias

    Version of Record online : 21 DEC 2005, DOI: 10.1002/prot.20770

  8. Minimal ensembles of side chain conformers for modeling protein–protein interactions

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 2, February 2012, Pages: 591–601, Dmitri Beglov, David R. Hall, Ryan Brenke, Maxim V. Shapovalov, Roland L. Dunbrack Jr., Dima Kozakov and Sandor Vajda

    Version of Record online : 22 NOV 2011, DOI: 10.1002/prot.23222

  9. Detailed analysis of grid-based molecular docking: A case study of CDOCKER—A CHARMm-based MD docking algorithm

    Journal of Computational Chemistry

    Volume 24, Issue 13, October 2003, Pages: 1549–1562, Guosheng Wu, Daniel H. Robertson, Charles L. Brooks III and Michal Vieth

    Version of Record online : 30 JUL 2003, DOI: 10.1002/jcc.10306

  10. Optimal design of protein docking potentials: Efficiency and limitations

    Proteins: Structure, Function, and Bioinformatics

    Volume 62, Issue 4, 1 March 2006, Pages: 970–981, Dror Tobi and Ivet Bahar

    Version of Record online : 29 DEC 2005, DOI: 10.1002/prot.20859

  11. The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals

    Journal of Computational Chemistry

    Volume 26, Issue 1, 15 January 2005, Pages: 48–71, Art E. Cho, John A. Wendel, Nagarajan Vaidehi, Peter M. Kekenes–Huskey, Wely B. Floriano, Prabal K. Maiti and William A. Goddard III

    Version of Record online : 4 NOV 2004, DOI: 10.1002/jcc.20118

  12. Surface-histogram: A new shape descriptor for protein-protein docking

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 1, January 2012, Pages: 221–238, Shengyin Gu, Patrice Koehl, Joel Hass and Nina Amenta

    Version of Record online : 9 NOV 2011, DOI: 10.1002/prot.23192

  13. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

    Journal of Computational Chemistry

    Volume 29, Issue 10, 30 July 2008, Pages: 1574–1588, Michal Brylinski and Jeffrey Skolnick

    Version of Record online : 21 FEB 2008, DOI: 10.1002/jcc.20917

  14. Flexible protein docking refinement using pose-dependent normal mode analysis

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 9, August 2012, Pages: 2262–2274, Vishwesh Venkatraman and David W. Ritchie

    Version of Record online : 18 JUN 2012, DOI: 10.1002/prot.24115

  15. Predicting protein complex geometries with a neural network

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 4, March 2010, Pages: 1026–1039, Myong-Ho Chae, Florian Krull, Stephan Lorenzen and Ernst-Walter Knapp

    Version of Record online : 8 OCT 2009, DOI: 10.1002/prot.22626

  16. Automatch: Target-binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 4, April 2012, Pages: 1078–1094, Changsheng Zhang and Luhua Lai

    Version of Record online : 7 JAN 2012, DOI: 10.1002/prot.24009

  17. You have full text access to this OnlineOpen article
    A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys

    Proteins: Structure, Function, and Bioinformatics

    Volume 69, Issue 2, 1 November 2007, Pages: 244–253, Shide Liang, Song Liu, Chi Zhang and Yaoqi Zhou

    Version of Record online : 10 JUL 2007, DOI: 10.1002/prot.21498

  18. Protein-protein docking by shape-complementarity and property matching

    Journal of Computational Chemistry

    Volume 31, Issue 9, 15 July 2010, Pages: 1919–1928, Tim Geppert, Ewgenij Proschak and Gisbert Schneider

    Version of Record online : 19 JAN 2010, DOI: 10.1002/jcc.21479

  19. MIAX: A new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases

    Proteins: Structure, Function, and Bioinformatics

    Volume 48, Issue 4, 1 September 2002, Pages: 696–732, Carlos Adriel Del Carpio-Muñoz, Eiichiro Ichiishi, Atsushi Yoshimori and Toshikazu Yoshikawa

    Version of Record online : 31 JUL 2002, DOI: 10.1002/prot.10122

  20. You have free access to this content
    Examination of shape complementarity in docking of Unbound proteins

    Proteins: Structure, Function, and Bioinformatics

    Volume 36, Issue 3, 15 August 1999, Pages: 307–317, Raquel Norel, Donald Petrey, Haim J. Wolfson and Ruth Nussinov

    Version of Record online : 1 OCT 1999, DOI: 10.1002/(SICI)1097-0134(19990815)36:3<307::AID-PROT5>3.0.CO;2-R