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There are 10718 results for: content related to: Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

  1. VoteDock: Consensus docking method for prediction of protein–ligand interactions

    Journal of Computational Chemistry

    Volume 32, Issue 4, March 2011, Pages: 568–581, Dariusz Plewczynski, Michał Łażniewski, Marcin Von Grotthuss, Leszek Rychlewski and Krzysztof Ginalski

    Version of Record online : 1 SEP 2010, DOI: 10.1002/jcc.21642

  2. Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes

    Journal of Computational Chemistry

    Volume 31, Issue 11, August 2010, Pages: 2109–2125, Xun Li, Yan Li, Tiejun Cheng, Zhihai Liu and Renxiao Wang

    Version of Record online : 1 FEB 2010, DOI: 10.1002/jcc.21498

  3. Modeling Complexes of Transmembrane Proteins: Systematic Analysis of Protein[BOND]Protein Docking Tools

    Molecular Informatics

    Volume 32, Issue 8, August 2013, Pages: 717–733, Agnieszka A. Kaczor, Jana Selent, Ferran Sanz and Manuel Pastor

    Version of Record online : 6 AUG 2013, DOI: 10.1002/minf.201200150

  4. Outstanding challenges in protein–ligand docking and structure-based virtual screening

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 1, Issue 2, March/April 2011, Pages: 229–259, Bohdan Waszkowycz, David E. Clark and Emanuela Gancia

    Version of Record online : 16 MAR 2011, DOI: 10.1002/wcms.18

  5. SKATE: A docking program that decouples systematic sampling from scoring

    Journal of Computational Chemistry

    Volume 31, Issue 14, 15 November 2010, Pages: 2540–2554, Jianwen A. Feng and Garland R. Marshall

    Version of Record online : 14 MAY 2010, DOI: 10.1002/jcc.21545

  6. Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

    Journal of Computational Chemistry

    Volume 34, Issue 11, 30 April 2013, Pages: 915–927, Xiaohua Zhang, Sergio E. Wong and Felice C. Lightstone

    Version of Record online : 23 JAN 2013, DOI: 10.1002/jcc.23214

  7. Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models

    Proteins: Structure, Function, and Bioinformatics

    Volume 60, Issue 4, 1 September 2005, Pages: 629–643, Simona Cotesta, Fabrizio Giordanetto, Jean-Yves Trosset, Patrizia Crivori, Romano T. Kroemer, Pieter F.W. Stouten and Anna Vulpetti

    Version of Record online : 18 JUL 2005, DOI: 10.1002/prot.20473

  8. 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

    Version of Record online : 6 OCT 2005, DOI: 10.1002/jcc.20292

  9. 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

  10. An iterative knowledge-based scoring function for protein–protein recognition

    Proteins: Structure, Function, and Bioinformatics

    Volume 72, Issue 2, 1 August 2008, Pages: 557–579, Sheng-You Huang and Xiaoqin Zou

    Version of Record online : 4 FEB 2008, DOI: 10.1002/prot.21949

  11. Docking and scoring with alternative side-chain conformations

    Proteins: Structure, Function, and Bioinformatics

    Volume 74, Issue 3, 15 February 2009, Pages: 712–726, Christoph Hartmann, Iris Antes and Thomas Lengauer

    Version of Record online : 14 AUG 2008, DOI: 10.1002/prot.22189

  12. You have free access to this content
    Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library

    Protein Science

    Volume 20, Issue 1, January 2011, Pages: 95–106, Yoshifumi Fukunishi and Haruki Nakamura

    Version of Record online : 10 DEC 2010, DOI: 10.1002/pro.540

  13. DynaDock: A new molecular dynamics-based algorithm for protein–peptide docking including receptor flexibility

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 5, April 2010, Pages: 1084–1104, Iris Antes

    Version of Record online : 16 OCT 2009, DOI: 10.1002/prot.22629

  14. PSI-DOCK: Towards highly efficient and accurate flexible ligand docking

    Proteins: Structure, Function, and Bioinformatics

    Volume 62, Issue 4, 1 March 2006, Pages: 934–946, Jianfeng Pei, Qi Wang, Zhenming Liu, Qingliang Li, Kun Yang and Luhua Lai

    Version of Record online : 4 JAN 2006, DOI: 10.1002/prot.20790

  15. Docking and Scoring in Drug Discovery

    Standard Article

    Burger's Medicinal Chemistry and Drug Discovery

    Francesca Spyrakis, Pietro Cozzini and Glen Eugene Kellogg

    Published Online : 15 SEP 2010, DOI: 10.1002/0471266949.bmc140

  16. EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

    Journal of Computational Chemistry

    Volume 22, Issue 15, 30 November 2001, Pages: 1750–1771, Yuan-Ping Pang, Emanuele Perola, Kun Xu and Franklyn G. Prendergast

    Version of Record online : 4 SEP 2001, DOI: 10.1002/jcc.1129

  17. Docking

    Computational Drug Design: A Guide for Computational and Medicinal Chemists

    David C. Young, Pages: 133–160, 2009

    Published Online : 25 FEB 2009, DOI: 10.1002/9780470451854.ch12

  18. Docking and Scoring Functions/Virtual Screening

    Standard Article

    Burger's Medicinal Chemistry and Drug Discovery

    Christoph Sotriffer, Gerhard Klebe, Martin Stahl and Hans-Joachim Böhm

    Published Online : 15 JAN 2003, DOI: 10.1002/0471266949.bmc007

  19. High quality binding modes in docking ligands to proteins

    Proteins: Structure, Function, and Bioinformatics

    Volume 71, Issue 3, 15 May 2008, Pages: 1373–1386, Boris Gorelik and Amiram Goldblum

    Version of Record online : 3 DEC 2007, DOI: 10.1002/prot.21847

  20. GalaxyDock2: Protein–ligand docking using beta-complex and global optimization

    Journal of Computational Chemistry

    Volume 34, Issue 30, 15 November 2013, Pages: 2647–2656, Woong-Hee Shin, Jae-Kwan Kim, Deok-Soo Kim and Chaok Seok

    Version of Record online : 23 SEP 2013, DOI: 10.1002/jcc.23438