Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

Supplement: Proteins

2007

Volume 69, Issue S8

Pages 1–207

  1. Editor's Corner

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
  2. CASP Introduction-Round VII

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have full text access to this OnlineOpen article
      Critical assessment of methods of protein structure prediction—Round VII (pages 3–9)

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

      Version of Record online: 5 OCT 2007 | DOI: 10.1002/prot.21767

  3. CASP7 Target Classification

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
      Domain definition and target classification for CASP7 (pages 10–18)

      Neil D. Clarke, Iakes Ezkurdia, Jürgen Kopp, Randy J. Read, Torsten Schwede and Michael Tress

      Version of Record online: 25 JUL 2007 | DOI: 10.1002/prot.21686

  4. Evaluation Measures

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have full text access to this OnlineOpen article
      New tools and expanded data analysis capabilities at the protein structure prediction center (pages 19–26)

      Andriy Kryshtafovych, Andreas Prlic, Zinoviy Dmytriv, Pawel Daniluk, Maciej Milostan, Volker Eyrich, Tim Hubbard and Krzysztof Fidelis

      Version of Record online: 17 AUG 2007 | DOI: 10.1002/prot.21653

  5. High Accuracy Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
  6. Template Based Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. Assessment of CASP7 predictions for template-based modeling targets (pages 38–56)

      Jürgen Kopp, Lorenza Bordoli, James N.D. Battey, Florian Kiefer and Torsten Schwede

      Version of Record online: 25 SEP 2007 | DOI: 10.1002/prot.21753

  7. New Folds: Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
      Assessment of CASP7 structure predictions for template free targets (pages 57–67)

      Ralf Jauch, Hock Chuan Yeo, Prasanna R. Kolatkar and Neil D. Clarke

      Version of Record online: 25 SEP 2007 | DOI: 10.1002/prot.21771

  8. New Folds: Server

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
      Automated server predictions in CASP7 (pages 68–82)

      James N. D. Battey, Jürgen Kopp, Lorenza Bordoli, Randy J. Read, Neil D. Clarke and Torsten Schwede

      Version of Record online: 25 SEP 2007 | DOI: 10.1002/prot.21761

  9. Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
      High accuracy template based modeling by global optimization (pages 83–89)

      Keehyoung Joo, Jinwoo Lee, Sunjoong Lee, Joo-Hyun Seo, Sung Jong Lee and Jooyoung Lee

      Version of Record online: 25 SEP 2007 | DOI: 10.1002/prot.21628

    2. You have free access to this content
      Analysis of TASSER-based CASP7 protein structure prediction results (pages 90–97)

      Hongyi Zhou, Shashi B. Pandit, Seung Yup Lee, Jose Borreguero, Huiling Chen, Liliana Wroblewska and Jeffrey Skolnick

      Version of Record online: 17 AUG 2007 | DOI: 10.1002/prot.21649

    3. You have free access to this content
      Fams-ace: A combined method to select the best model after remodeling all server models (pages 98–107)

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

      Version of Record online: 25 SEP 2007 | DOI: 10.1002/prot.21785

    4. You have free access to this content
    5. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home (pages 118–128)

      Rhiju Das, Bin Qian, Srivatsan Raman, Robert Vernon, James Thompson, Philip Bradley, Sagar Khare, Michael D. Tyka, Divya Bhat, Dylan Chivian, David E. Kim, William H. Sheffler, Lars Malmström, Andrew M. Wollacott, Chu Wang, Ingemar Andre and David Baker

      Version of Record online: 25 SEP 2007 | DOI: 10.1002/prot.21636

  10. Disorder: Predictions

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. Assessment of disorder predictions in CASP7 (pages 129–136)

      Lorenza Bordoli, Florian Kiefer and Torsten Schwede

      Version of Record online: 6 AUG 2007 | DOI: 10.1002/prot.21671

  11. Domain: Predictions

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. Assessment of predictions submitted for the CASP7 domain prediction category (pages 137–151)

      Michael Tress, Jianlin Cheng, Pierre Baldi, Keehyoung Joo, Jinwoo Lee, Joo-Hyun Seo, Jooyoung Lee, David Baker, Dylan Chivian, David Kim and Iakes Ezkurdia

      Version of Record online: 6 AUG 2007 | DOI: 10.1002/prot.21675

  12. Contact: Assessment

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
      Assessment of intramolecular contact predictions for CASP7 (pages 152–158)

      José M. G. Izarzugaza, Osvaldo Graña, Michael L. Tress, Alfonso Valencia and Neil D. Clarke

      Version of Record online: 1 AUG 2007 | DOI: 10.1002/prot.21637

  13. Contact: Predictions

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
      Contact prediction using mutual information and neural nets (pages 159–164)

      George Shackelford and Kevin Karplus

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21791

  14. Function: Predictions

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
      Assessment of predictions submitted for the CASP7 function prediction category (pages 165–174)

      Gonzalo López, Ana Rojas, Michael Tress and Alfonso Valencia

      Version of Record online: 24 JUL 2007 | DOI: 10.1002/prot.21651

  15. Quality Assessments

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. Assessment of predictions in the model quality assessment category (pages 175–183)

      Domenico Cozzetto, Andriy Kryshtafovych, Michele Ceriani and Anna Tramontano

      Version of Record online: 6 AUG 2007 | DOI: 10.1002/prot.21669

  16. Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
  17. CASP Progress Reports

    1. Top of page
    2. Editor's Corner
    3. CASP Introduction-Round VII
    4. CASP7 Target Classification
    5. Evaluation Measures
    6. High Accuracy Assessment
    7. Template Based Assessment
    8. New Folds: Assessment
    9. New Folds: Server
    10. Prediction Reports
    11. Disorder: Predictions
    12. Domain: Predictions
    13. Contact: Assessment
    14. Contact: Predictions
    15. Function: Predictions
    16. Quality Assessments
    17. Prediction Reports
    18. CASP Progress Reports
    1. You have free access to this content
      Progress from CASP6 to CASP7 (pages 194–207)

      Andriy Kryshtafovych, Krzysztof Fidelis and John Moult

      Version of Record online: 5 OCT 2007 | DOI: 10.1002/prot.21769

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