Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

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

15 November 2010

Volume 78, Issue 15

Pages 3065–3249

  1. Editor's Corner

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Report
    5. Research Articles
    6. Prediction Reports
    7. Research Articles
    8. Prediction Reports
    9. Research Articles
  2. Research Articles

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Report
    5. Research Articles
    6. Prediction Reports
    7. Research Articles
    8. Prediction Reports
    9. Research Articles
    1. Docking and scoring protein interactions: CAPRI 2009 (pages 3073–3084)

      Marc F. Lensink and Shoshana J. Wodak

      Version of Record online: 14 JUL 2010 | DOI: 10.1002/prot.22818

    2. Performance of ZDOCK and ZRANK in CAPRI rounds 13–19 (pages 3104–3110)

      Howook Hwang, Thom Vreven, Brian G. Pierce, Jui-Hung Hung and Zhiping Weng

      Version of Record online: 11 MAY 2010 | DOI: 10.1002/prot.22764

    3. Protein–protein docking benchmark version 4.0 (pages 3111–3114)

      Howook Hwang, Thom Vreven, Joël Janin and Zhiping Weng

      Version of Record online: 23 JUL 2010 | DOI: 10.1002/prot.22830

    4. A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13–19 (pages 3115–3123)

      Aroop Sircar, Sidhartha Chaudhury, Krishna Praneeth Kilambi, Monica Berrondo and Jeffrey J. Gray

      Version of Record online: 18 MAY 2010 | DOI: 10.1002/prot.22765

    5. Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19 (pages 3124–3130)

      Dima Kozakov, David R. Hall, Dmitri Beglov, Ryan Brenke, Stephen R. Comeau, Yang Shen, Keyong Li, Jiefu Zheng, Pirooz Vakili, Ioannis Ch. Paschalidis and Sandor Vajda

      Version of Record online: 23 JUL 2010 | DOI: 10.1002/prot.22835

    6. Can self-inhibitory peptides be derived from the interfaces of globular protein–protein interactions? (pages 3140–3149)

      Nir London, Barak Raveh, Dana Movshovitz-Attias and Ora Schueler-Furman

      Version of Record online: 1 JUN 2010 | DOI: 10.1002/prot.22785

    7. Protein–protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring (pages 3150–3155)

      Xinqi Gong, Panwen Wang, Feng Yang, Shan Chang, Bin Liu, Hongqiu He, Libin Cao, Xianjin Xu, Chunhua Li, Weizu Chen and Cunxin Wang

      Version of Record online: 23 JUL 2010 | DOI: 10.1002/prot.22831

  3. Prediction Report

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Report
    5. Research Articles
    6. Prediction Reports
    7. Research Articles
    8. Prediction Reports
    9. Research Articles
    1. ReplicOpter: A replicate optimizer for flexible docking (pages 3156–3165)

      Omar N. A. Demerdash, Amanda Buyan and Julie C Mitchell

      Version of Record online: 29 JUN 2010 | DOI: 10.1002/prot.22811

  4. Research Articles

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Report
    5. Research Articles
    6. Prediction Reports
    7. Research Articles
    8. Prediction Reports
    9. Research Articles
    1. Selection of near-native poses in CAPRI rounds 13-19 (pages 3166–3173)

      Sanbo Qin and Huan-Xiang Zhou

      Version of Record online: 20 MAY 2010 | DOI: 10.1002/prot.22772

    2. CAPRI targets T29–T42: Proving ground for new docking procedures (pages 3174–3181)

      Miriam Eisenstein, Avraham Ben-Shimon, Ziv Frankenstein and Noga Kowalsman

      Version of Record online: 10 JUN 2010 | DOI: 10.1002/prot.22793

    3. Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain–domain assembly and protein-RNA binding (pages 3182–3188)

      Carles Pons, Albert Solernou, Laura Perez-Cano, Solène Grosdidier and Juan Fernandez-Recio

      Version of Record online: 20 MAY 2010 | DOI: 10.1002/prot.22773

  5. Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Report
    5. Research Articles
    6. Prediction Reports
    7. Research Articles
    8. Prediction Reports
    9. Research Articles
    1. An integrated suite of fast docking algorithms (pages 3197–3204)

      Efrat Mashiach, Dina Schneidman-Duhovny, Aviyah Peri, Yoli Shavit, Ruth Nussinov and Haim J. Wolfson

      Version of Record online: 8 JUN 2010 | DOI: 10.1002/prot.22790

  6. Research Articles

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Report
    5. Research Articles
    6. Prediction Reports
    7. Research Articles
    8. Prediction Reports
    9. Research Articles
    1. You have full text access to this OnlineOpen article
      Rosetta in CAPRI rounds 13–19 (pages 3212–3218)

      Sarel J. Fleishman, Jacob E. Corn, Eva M. Strauch, Tim A. Whitehead, Ingemar Andre, James Thompson, James J. Havranek, Rhiju Das, Philip Bradley and David Baker

      Version of Record online: 1 JUN 2010 | DOI: 10.1002/prot.22784

    2. Side-chain rotamer transitions at protein-protein interfaces (pages 3219–3225)

      Mainak Guharoy, Joël Janin and Charles H. Robert

      Version of Record online: 14 JUL 2010 | DOI: 10.1002/prot.22821

  7. Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Report
    5. Research Articles
    6. Prediction Reports
    7. Research Articles
    8. Prediction Reports
    9. Research Articles
  8. Research Articles

    1. Top of page
    2. Editor's Corner
    3. Research Articles
    4. Prediction Report
    5. Research Articles
    6. Prediction Reports
    7. Research Articles
    8. Prediction Reports
    9. Research Articles
    1. Docking by structural similarity at protein-protein interfaces (pages 3235–3241)

      Rohita Sinha, Petras J. Kundrotas and Ilya A. Vakser

      Version of Record online: 29 JUN 2010 | DOI: 10.1002/prot.22812

    2. Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions (pages 3242–3249)

      Sjoerd J. de Vries, Adrien S. J. Melquiond, Panagiotis L. Kastritis, Ezgi Karaca, Annalisa Bordogna, Marc van Dijk, João P. G. L. M. Rodrigues and Alexandre M. J. J. Bonvin

      Version of Record online: 6 JUL 2010 | DOI: 10.1002/prot.22814

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