Proteins: Structure, Function, and Bioinformatics

Copyright © 2013 Wiley Periodicals Inc.

Cover image for Proteins: Structure, Function, and Bioinformatics

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

1 August 2005

Volume 60, Issue 2

Pages 149–323

Issue edited by: Joël Janin

  1. Editor's Corner

    1. Top of page
    2. Editor's Corner
    3. Research Article
    1. Sailing the route from Gaeta, Italy, to CAPRI (page 149)

      Joël Janin

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20552

  2. Research Article

    1. Top of page
    2. Editor's Corner
    3. Research Article
    1. Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures (pages 150–169)

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

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20551

    2. The targets of CAPRI rounds 3–5 (pages 170–175)

      Joël Janin

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20553

    3. Classification of protein complexes based on docking difficulty (pages 176–180)

      Sandor Vajda

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20554

    4. CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock (pages 181–186)

      Michael D. Daily, David Masica, Arvind Sivasubramanian, Sony Somarouthu and Jeffrey J. Gray

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20555

    5. Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility (pages 187–194)

      Ora Schueler-Furman, Chu Wang and David Baker

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20556

    6. Docking to single-domain and multiple-domain proteins: Old and new challenges (pages 195–201)

      E. Ben-Zeev, N. Kowalsman, A. Ben-Shimon, D. Segal, T. Atarot, O. Noivirt, T. Shay and M. Eisenstein

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20557

    7. Modeling oligomers with Cn or Dn symmetry: Application to CAPRI target 10 (pages 202–206)

      Alexander Berchanski, Dadi Segal and Miriam Eisenstein

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20558

    8. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5 (pages 207–213)

      Kevin Wiehe, Brian Pierce, Julian Mintseris, Wei Wei Tong, Robert Anderson, Rong Chen and Zhiping Weng

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20559

    9. Protein–protein docking benchmark 2.0: An update (pages 214–216)

      Julian Mintseris, Kevin Wiehe, Brian Pierce, Robert Anderson, Rong Chen, Joël Janin and Zhiping Weng

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20560

    10. Approaching the CAPRI challenge with an efficient geometry-based docking (pages 217–223)

      Yuval Inbar, Dina Schneidman-Duhovny, Inbal Halperin, Assaf Oron, Ruth Nussinov and Haim J. Wolfson

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20561

    11. Geometry-based flexible and symmetric protein docking (pages 224–231)

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

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20562

    12. Data-driven docking: HADDOCK's adventures in CAPRI (pages 232–238)

      A. D. J. van Dijk, S. J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou and A. M. J. J. Bonvin

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20563

    13. Performance of the first protein docking server ClusPro in CAPRI rounds 3–5 (pages 239–244)

      Stephen R. Comeau, Sandor Vajda and Carlos J. Camacho

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20564

    14. Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets (pages 245–251)

      Carlos J. Camacho

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20565

    15. ATTRACT: Protein–protein docking in CAPRI using a reduced protein model (pages 252–256)

      Martin Zacharias

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20566

    16. Study of protein–protein interaction using conformational space annealing (pages 257–262)

      Kyoungrim Lee, Jaehyun Sim and Jooyoung Lee

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20567

    17. Incorporation of flexibility into rigid-body docking: Applications in rounds 3–5 of CAPRI (pages 263–268)

      Graham R. Smith, Paul W. Fitzjohn, Christopher S. Page and Paul A. Bates

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20568

    18. Docking essential dynamics eigenstructures (pages 269–274)

      Diana Mustard and David W. Ritchie

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20569

    19. Scoring docking models with evolutionary information (pages 275–280)

      Michael Tress, David de Juan, Osvaldo Graña, Manuel J. Gómez, Paulino Gómez-Puertas, Jose M. González, Gonzalo López and Alfonso Valencia

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20570

    20. Protein–protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI (pages 281–288)

      Phil Carter, Victor I. Lesk, Suhail A. Islam and Michael J.E. Sternberg

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20571

    21. Searching for protein–protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues (pages 289–295)

      Genki Terashi, Mayuko Takeda-Shitaka, Daisuke Takaya, Katsuichiro Komatsu and Hideaki Umeyama

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20572

    22. Development and testing of an automated approach to protein docking (pages 296–301)

      Andrei Tovchigrechko and Ilya A. Vakser

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20573

    23. Progress in computation and amide hydrogen exchange for prediction of protein–protein complexes (pages 302–307)

      Dennis Law, Matthew Hotchko and Lynn Ten Eyck

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20574

    24. Improving CAPRI predictions: Optimized desolvation for rigid-body docking (pages 308–313)

      Juan Fernández-Recio, Ruben Abagyan and Maxim Totrov

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20575

    25. Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function (pages 314–318)

      Chi Zhang, Song Liu and Yaoqi Zhou

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20576

    26. Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition (pages 319–323)

      Xiao Hui Ma, Chun Hua Li, Long Zhu Shen, Xin Qi Gong, Wei Zu Chen and Cun Xin Wang

      Article first published online: 24 JUN 2005 | DOI: 10.1002/prot.20577

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