Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

Special Issue: Third Meeting on the Critical Assessment of PRedicted Interactions

December 2007

Volume 69, Issue 4

Pages 697–872

  1. Editor's Corner

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Reports
    5. Research Articles
  2. Research Articles

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Reports
    5. Research Articles
  3. Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Reports
    5. Research Articles
  4. Research Articles

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Reports
    5. Research Articles
    1. The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI (pages 719–725)

      Kevin Wiehe, Brian Pierce, Wei Wei Tong, Howook Hwang, Julian Mintseris and Zhiping Weng

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21747

    2. HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets (pages 726–733)

      Sjoerd J. de Vries, Aalt D. J. van Dijk, Mickaël Krzeminski, Mark van Dijk, Aurelien Thureau, Victor Hsu, Tsjerk Wassenaar and Alexandre M. J. J. Bonvin

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21723

    3. Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI (pages 734–742)

      Yang Shen, Ryan Brenke, Dima Kozakov, Stephen R. Comeau, Dmitri Beglov and Sandor Vajda

      Article first published online: 12 SEP 2007 | DOI: 10.1002/prot.21754

    4. A holistic approach to protein docking (pages 743–749)

      Sanbo Qin and Huan-Xiang Zhou

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21752

    5. Implicit flexibility in protein docking: Cross-docking and local refinement (pages 750–757)

      Marcin Król, Raphael A. G. Chaleil, Alexander L. Tournier and Paul A. Bates

      Article first published online: 1 AUG 2007 | DOI: 10.1002/prot.21698

    6. RosettaDock in CAPRI rounds 6–12 (pages 758–763)

      Chu Wang, Ora Schueler-Furman, Ingemar Andre, Nir London, Sarel J. Fleishman, Philip Bradley, Bin Qian and David Baker

      Article first published online: 1 AUG 2007 | DOI: 10.1002/prot.21684

    7. Automatic prediction of protein interactions with large scale motion (pages 764–773)

      Dina Schneidman-Duhovny, Ruth Nussinov and Haim J. Wolfson

      Article first published online: 20 SEP 2007 | DOI: 10.1002/prot.21759

    8. ClusPro: Performance in CAPRI rounds 6–11 and the new server (pages 781–785)

      Stephen R. Comeau, Dima Kozakov, Ryan Brenke, Yang Shen, Dmitri Beglov and Sandor Vajda

      Article first published online: 17 SEP 2007 | DOI: 10.1002/prot.21795

    9. Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6–12 (pages 793–800)

      Sidhartha Chaudhury, Aroop Sircar, Arvind Sivasubramanian, Monica Berrondo and Jeffrey J. Gray

      Article first published online: 25 SEP 2007 | DOI: 10.1002/prot.21731

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    11. Docking of protein molecular surfaces with evolutionary trace analysis (pages 832–838)

      Eiji Kanamori, Yoichi Murakami, Yuko Tsuchiya, Daron M. Standley, Haruki Nakamura and Kengo Kinoshita

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21737

    12. Docking without docking: ISEARCH—prediction of interactions using known interfaces (pages 839–844)

      Stefan Günther, Patrick May, Andreas Hoppe, Cornelius Frömmel and Robert Preissner

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21746

    13. DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking (pages 845–851)

      Ying Gao, Dominique Douguet, Andrey Tovchigrechko and Ilya A. Vakser

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21714

    14. Prediction and scoring of docking poses with pyDock (pages 852–858)

      Solène Grosdidier, Carles Pons, Albert Solernou and Juan Fernández-Recio

      Article first published online: 17 SEP 2007 | DOI: 10.1002/prot.21796

    15. A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI (pages 859–865)

      Xin Qi Gong, Shan Chang, Qing Hua Zhang, Chun Hua Li, Long Zhu Shen, Xiao Hui Ma, Ming Hui Wang, Bin Liu, Hong Qiu He, Wei Zu Chen and Cun Xin Wang

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21738

    16. The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation (pages 866–872)

      Genki Terashi, Mayuko Takeda-Shitaka, Kazuhiko Kanou, Mitsuo Iwadate, Daisuke Takaya and Hideaki Umeyama

      Article first published online: 12 SEP 2007 | DOI: 10.1002/prot.21772

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