Proteins: Structure, Function, and Bioinformatics

Copyright © 2013 Wiley Periodicals Inc.

Cover image for Proteins: Structure, Function, and Bioinformatics

Supplement: Proteins

2009

Volume 77, Issue S9

Pages 1–228

  1. CASP Introduction—Round VIII

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Critical assessment of methods of protein structure prediction—Round VIII (pages 1–4)

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

      Article first published online: 21 AUG 2009 | DOI: 10.1002/prot.22589

  2. Evaluation Measures

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Protein structure prediction center in CASP8 (pages 5–9)

      Andriy Kryshtafovych, Oleh Krysko, Pawel Daniluk, Zinovii Dmytriv and Krzysztof Fidelis

      Article first published online: 6 JUL 2009 | DOI: 10.1002/prot.22517

  3. CASP8 Target Classification

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Target domain definition and classification in CASP8 (pages 10–17)

      Michael L. Tress, Iakes Ezkurdia and Jane S. Richardson

      Article first published online: 9 JUN 2009 | DOI: 10.1002/prot.22497

  4. Template Based Assessment

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Evaluation of template-based models in CASP8 with standard measures (pages 18–28)

      Domenico Cozzetto, Andriy Kryshtafovych, Krzysztof Fidelis, John Moult, Burkhard Rost and Anna Tramontano

      Article first published online: 5 AUG 2009 | DOI: 10.1002/prot.22561

    2. You have free access to this content
      The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models (pages 29–49)

      Daniel A. Keedy, Christopher J. Williams, Jeffrey J. Headd, W. Bryan Arendall III, Vincent B. Chen, Gary J. Kapral, Robert A. Gillespie, Jeremy N. Block, Adam Zemla, David C. Richardson and Jane S. Richardson

      Article first published online: 20 JUL 2009 | DOI: 10.1002/prot.22551

  5. New Folds: Assessment

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Assessment of CASP8 structure predictions for template free targets (pages 50–65)

      Moshe Ben-David, Orly Noivirt-Brik, Aviv Paz, Jaime Prilusky, Joel L. Sussman and Yaakov Levy

      Article first published online: 21 AUG 2009 | DOI: 10.1002/prot.22591

  6. High Accuracy Assessment

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Assessment of the protein-structure refinement category in CASP8 (pages 66–80)

      Justin L. MacCallum, Lan Hua, Michael J. Schnieders, Vijay S. Pande, Matthew P. Jacobson and Ken A. Dill

      Article first published online: 20 JUL 2009 | DOI: 10.1002/prot.22538

  7. Prediction Reports

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins (pages 81–88)

      Česlovas Venclovas and Mindaugas Margelevičius

      Article first published online: 22 JUN 2009 | DOI: 10.1002/prot.22515

    2. You have free access to this content
      Structure prediction for CASP8 with all-atom refinement using Rosetta (pages 89–99)

      Srivatsan Raman, Robert Vernon, James Thompson, Michael Tyka, Ruslan Sadreyev, Jimin Pei, David Kim, Elizabeth Kellogg, Frank DiMaio, Oliver Lange, Lisa Kinch, Will Sheffler, Bong-Hyun Kim, Rhiju Das, Nick V. Grishin and David Baker

      Article first published online: 20 JUL 2009 | DOI: 10.1002/prot.22540

    3. You have free access to this content
      I-TASSER: Fully automated protein structure prediction in CASP8 (pages 100–113)

      Yang Zhang

      Article first published online: 21 AUG 2009 | DOI: 10.1002/prot.22588

    4. You have free access to this content
      Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8 (pages 114–122)

      Elmar Krieger, Keehyoung Joo, Jinwoo Lee, Jooyoung Lee, Srivatsan Raman, James Thompson, Mike Tyka, David Baker and Kevin Karplus

      Article first published online: 12 AUG 2009 | DOI: 10.1002/prot.22570

    5. You have free access to this content
      Performance of the Pro-sp3-TASSER server in CASP8 (pages 123–127)

      Hongyi Zhou, Shashi B. Pandit and Jeffrey Skolnick

      Article first published online: 17 JUN 2009 | DOI: 10.1002/prot.22501

    6. You have free access to this content
      Fast and accurate automatic structure prediction with HHpred (pages 128–132)

      Andrea Hildebrand, Michael Remmert, Andreas Biegert and Johannes Söding

      Article first published online: 17 JUN 2009 | DOI: 10.1002/prot.22499

    7. You have free access to this content
      Template-based and free modeling by RAPTOR++ in CASP8 (pages 133–137)

      Jinbo Xu, Jian Peng and Feng Zhao

      Article first published online: 5 AUG 2009 | DOI: 10.1002/prot.22567

  8. Function: Assessment

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Assessment of ligand binding residue predictions in CASP8 (pages 138–146)

      Gonzalo López, Iakes Ezkurdia and Michael L. Tress

      Article first published online: 22 JUL 2009 | DOI: 10.1002/prot.22557

  9. Function: Predictions

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Prediction of ligand binding sites using homologous structures and conservation at CASP8 (pages 147–151)

      Mark N. Wass and Michael J. E. Sternberg

      Article first published online: 19 JUN 2009 | DOI: 10.1002/prot.22513

    2. You have free access to this content
      Protein-binding site prediction based on three-dimensional protein modeling (pages 152–156)

      Mina Oh, Keehyoung Joo and Jooyoung Lee

      Article first published online: 12 AUG 2009 | DOI: 10.1002/prot.22572

  10. Quality: Assessment

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Evaluation of CASP8 model quality predictions (pages 157–166)

      Domenico Cozzetto, Andriy Kryshtafovych and Anna Tramontano

      Article first published online: 14 JUL 2009 | DOI: 10.1002/prot.22534

  11. Quality: Predictions

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Assessment of global and local model quality in CASP8 using Pcons and ProQ (pages 167–172)

      Per Larsson, Marcin J. Skwark, Björn Wallner and Arne Elofsson

      Article first published online: 11 MAY 2009 | DOI: 10.1002/prot.22476

    2. You have free access to this content
      Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust (pages 173–180)

      Pascal Benkert, Silvio C. E. Tosatto and Torsten Schwede

      Article first published online: 14 JUL 2009 | DOI: 10.1002/prot.22532

    3. You have free access to this content
      Prediction of global and local quality of CASP8 models by MULTICOM series (pages 181–184)

      Jianlin Cheng, Zheng Wang, Allison N. Tegge and Jesse Eickholt

      Article first published online: 28 MAY 2009 | DOI: 10.1002/prot.22487

    4. You have free access to this content
      Prediction of global and local model quality in CASP8 using the ModFOLD server (pages 185–190)

      Liam J. McGuffin

      Article first published online: 2 JUN 2009 | DOI: 10.1002/prot.22491

    5. You have free access to this content
      Applying Undertaker to quality assessment (pages 191–195)

      John G. Archie, Martin Paluszewski and Kevin Karplus

      Article first published online: 19 JUN 2009 | DOI: 10.1002/prot.22508

  12. Domain and Contacts: Assessment

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8 (pages 196–209)

      Iakes Ezkurdia, Osvaldo Graña, José M. G. Izarzugaza and Michael L. Tress

      Article first published online: 24 JUL 2009 | DOI: 10.1002/prot.22554

  13. Disorder: Assessment

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      Assessment of disorder predictions in CASP8 (pages 210–216)

      Orly Noivirt-Brik, Jaime Prilusky and Joel L. Sussman

      Article first published online: 21 AUG 2009 | DOI: 10.1002/prot.22586

  14. CASP Progress Reports

    1. Top of page
    2. CASP Introduction—Round VIII
    3. Evaluation Measures
    4. CASP8 Target Classification
    5. Template Based Assessment
    6. New Folds: Assessment
    7. High Accuracy Assessment
    8. Prediction Reports
    9. Function: Assessment
    10. Function: Predictions
    11. Quality: Assessment
    12. Quality: Predictions
    13. Domain and Contacts: Assessment
    14. Disorder: Assessment
    15. CASP Progress Reports
    1. You have free access to this content
      CASP8 results in context of previous experiments (pages 217–228)

      Andriy Kryshtafovych, Krzysztof Fidelis and John Moult

      Article first published online: 5 AUG 2009 | DOI: 10.1002/prot.22562

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