Proteins: Structure, Function, and Bioinformatics

Copyright © 2013 Wiley Periodicals Inc.

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
    1. From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent (pages 697–698)

      Shoshana J. Wodak

      Article first published online: 2 OCT 2007 | DOI: 10.1002/prot.21805

  2. Research Articles

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Reports
    5. Research Articles
    1. The targets of CAPRI rounds 6–12 (pages 699–703)

      Joël Janin

      Article first published online: 1 AUG 2007 | DOI: 10.1002/prot.21689

  3. Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Reports
    5. Research Articles
    1. Docking and scoring protein complexes: CAPRI 3rd Edition (pages 704–718)

      Marc F. Lensink, Raúl Méndez and Shoshana J. Wodak

      Article first published online: 5 OCT 2007 | DOI: 10.1002/prot.21804

  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. Protein–protein docking in CAPRI using ATTRACT to account for global and local flexibility (pages 774–780)

      Andreas May and Martin Zacharias

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21735

    9. 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

    10. Acidic groups docked to well defined wetted pockets at the core of the binding interface: A tale of scoring and missing protein interactions in CAPRI (pages 786–792)

      Marta Bueno and Carlos J. Camacho

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21722

    11. 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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      SOFTDOCK application to protein–protein interaction benchmark and CAPRI (pages 801–808)

      Nan Li, Zhonghua Sun and Fan Jiang

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21728

    13. Assessing the energy landscape of CAPRI targets by FunHunt (pages 809–815)

      Nir London and Ora Schueler-Furman

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21736

    14. Protein–protein docking: Progress in CAPRI rounds 6–12 using a combination of methods: The introduction of steered solvated molecular dynamics (pages 816–822)

      Alexander Heifetz, Sandeep Pal and Graham R. Smith

      Article first published online: 5 SEP 2007 | DOI: 10.1002/prot.21734

    15. A general approach for developing system-specific functions to score protein–ligand docked complexes using support vector inductive logic programming (pages 823–831)

      Ata Amini, Paul J. Shrimpton, Stephen H. Muggleton and Michael J. E. Sternberg

      Article first published online: 1 OCT 2007 | DOI: 10.1002/prot.21782

    16. 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

    17. 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

    18. 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

    19. 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

    20. 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

    21. 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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