Proteins: Structure, Function, and Bioinformatics

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. 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

    4. 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

    5. 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

    6. 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

    7. 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

    8. 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

    9. 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

    10. 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

    11. 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

    12. 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

    13. 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

    14. 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

    15. 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

    16. 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

    17. 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

    18. 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

    19. 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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