Proteins: Structure, Function, and Bioinformatics

Cover image for Vol. 61 Issue S7

Supplement: Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction

2005

Volume 61, Issue S7

Pages 1–236

  1. Editor's Corner

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
  2. CASP Introduction

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Critical assessment of methods of protein structure prediction (CASP)—Round 6 (pages 3–7)

      John Moult, Krzysztof Fidelis, Burkhard Rost, Tim Hubbard and Anna Tramontano

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20716

  3. CASP6 Definitions and Classifications

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Domain definition and target classification for CASP6 (pages 8–18)

      Michael Tress, Chin-Hsien Tai, Guoli Wang, Iakes Ezkurdia, Gonzalo López, Alfonso Valencia, Byungkook Lee and Roland L. Dunbrack Jr.

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20717

  4. Automated Evaluation of Predictions

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. CASP6 data processing and automatic evaluation at the protein structure prediction center (pages 19–23)

      Andriy Kryshtafovych, Maciej Milostan, Lukasz Szajkowski, Pawel Daniluk and Krzysztof Fidelis

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20718

  5. Automated Server Data Collection

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. System for accepting server predictions in CASP6 (pages 24–26)

      Volker A. Eyrich, Andriy Kryshtafovych, Maciej Milostan and Krzysztof Fidelis

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20719

  6. Comparative Modeling: Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Assessment of predictions submitted for the CASP6 comparative modeling category (pages 27–45)

      Michael Tress, Iakes Ezkurdia, Osvaldo Graña, Gonzalo López and Alfonso Valencia

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20720

  7. Fold Recognition: Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Assessment of fold recognition predictions in CASP6 (pages 46–66)

      Guoli Wang, Yumi Jin and Roland L. Dunbrack Jr.

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20721

  8. New Folds: Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Assessment of CASP6 predictions for new and nearly new fold targets (pages 67–83)

      James J. Vincent, Chin-Hsien Tai, B.K. Sathyanarayana and Byungkook Lee

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20722

  9. Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. TASSER: An automated method for the prediction of protein tertiary structures in CASP6 (pages 91–98)

      Yang Zhang, Adrian K. Arakaki and Jeffrey Skolnick

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20724

    2. FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6 (pages 106–113)

      Jan Kosinski, Michal J. Gajda, Iwona A. Cymerman, Michal A. Kurowski, Marcin Pawlowski, Michal Boniecki, Agnieszka Obarska, Grzegorz Papaj, Paulina Sroczynska-Obuchowicz, Karolina L. Tkaczuk, Paulina Sniezynska, Joanna M. Sasin, Anna Augustyn, Janusz M. Bujnicki and Marcin Feder

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20726

    3. Protein structure prediction using a variety of profile libraries and 3D verification (pages 114–121)

      Kentaro Tomii, Takatsugu Hirokawa and Chie Motono

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20727

    4. Protein structure prediction in CASP6 using CHIMERA and FAMS (pages 122–127)

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

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20728

    5. Free modeling with Rosetta in CASP6 (pages 128–134)

      Philip Bradley, Lars Malmström, Bin Qian, Jack Schonbrun, Dylan Chivian, David E. Kim, Jens Meiler, Kira M.S. Misura and David Baker

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20729

    6. SAM-T04: What is new in protein–structure prediction for CASP6 (pages 135–142)

      Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano and Richard Hughey

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20730

    7. Prediction of novel and analogous folds using fragment assembly and fold recognition (pages 143–151)

      D. T. Jones, K. Bryson, A. Coleman, L. J. McGuffin, M. I. Sadowski, J. S. Sodhi and J. J. Ward

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20731

  10. Automated Servers Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. SPARKS 2 and SP3 servers in CASP6 (pages 152–156)

      Hongyi Zhou and Yaoqi Zhou

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20732

  11. Automated Servers: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Prediction of CASP6 structures using automated robetta protocols (pages 157–166)

      Dylan Chivian, David E. Kim, Lars Malmström, Jack Schonbrun, Carol A. Rohl and David Baker

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20733

  12. Disordered Regions: Assessments

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Assessment of disorder predictions in CASP6 (pages 167–175)

      Yumi Jin and Roland L. Dunbrack Jr.

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20734

  13. Disordered Regions: Prediction Report

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Exploiting heterogeneous sequence properties improves prediction of protein disorder (pages 176–182)

      Zoran Obradovic, Kang Peng, Slobodan Vucetic, Predrag Radivojac and A. Keith Dunker

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20735

  14. Domain Boundaries: Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Evaluation of domain prediction in CASP6 (pages 183–192)

      Chin-Hsien Tai, Woei-Jyh Lee, James J. Vincent and Byungkook Lee

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20736

  15. Domain Boundaries: Prediction Report

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM (pages 193–200)

      David E. Kim, Dylan Chivian, Lars Malmström and David Baker

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20737

  16. Protein Function: Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. The prediction of protein function at CASP6 (pages 201–213)

      Simonetta Soro and Anna Tramontano

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20738

  17. Contacts: Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. CASP6 assessment of contact prediction (pages 214–224)

      Osvaldo Graña, David Baker, Robert M. MacCallum, Jens Meiler, Marco Punta, Burkhard Rost, Michael L. Tress and Alfonso Valencia

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20739

  18. CASP Progress Report

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction
    4. CASP6 Definitions and Classifications
    5. Automated Evaluation of Predictions
    6. Automated Server Data Collection
    7. Comparative Modeling: Assessment
    8. Fold Recognition: Assessment
    9. New Folds: Assessment
    10. Prediction Reports
    11. Automated Servers Prediction Reports
    12. Automated Servers: Prediction Reports
    13. Disordered Regions: Assessments
    14. Disordered Regions: Prediction Report
    15. Domain Boundaries: Assessment
    16. Domain Boundaries: Prediction Report
    17. Protein Function: Assessment
    18. Contacts: Assessment
    19. CASP Progress Report
    1. Progress over the first decade of CASP experiments (pages 225–236)

      Andriy Kryshtafovych, Česlovas Venclovas, Krzysztof Fidelis and John Moult

      Version of Record online: 26 SEP 2005 | DOI: 10.1002/prot.20740

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