Proteins: Structure, Function, and Bioinformatics

Copyright © 2013 Wiley Periodicals Inc.

Cover image for Vol. 79 Issue S10

Supplement: PROTEINS

2011

Volume 79, Issue S10

Pages 1–207

  1. CASP Introduction—Round IX

    1. Top of page
    2. CASP Introduction—Round IX
    3. CASP Targets
    4. Template Based Assessment
    5. Free Modeling Assessment
    6. Refinement Assessment
    7. Assessment of Other Categories of Predictions
    8. Prediction Methods and Reports
    9. CASP Progress Reports
    1. Critical assessment of methods of protein structure prediction (CASP)—round IX (pages 1–5)

      John Moult, Krzysztof Fidelis, Andriy Kryshtafovych and Anna Tramontano

      Article first published online: 14 OCT 2011 | DOI: 10.1002/prot.23200

  2. CASP Targets

    1. Top of page
    2. CASP Introduction—Round IX
    3. CASP Targets
    4. Template Based Assessment
    5. Free Modeling Assessment
    6. Refinement Assessment
    7. Assessment of Other Categories of Predictions
    8. Prediction Methods and Reports
    9. CASP Progress Reports
    1. Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction (pages 6–20)

      Andriy Kryshtafovych, John Moult, Sergio G. Bartual, J. Fernando Bazan, Helen Berman, Darren E. Casteel, Evangelos Christodoulou, John K. Everett, Jens Hausmann, Tatjana Heidebrecht, Tanya Hills, Raymond Hui, John F. Hunt, Jayaraman Seetharaman, Andrzej Joachimiak, Michael A. Kennedy, Choel Kim, Andreas Lingel, Karolina Michalska, Gaetano T. Montelione, José M. Otero, Anastassis Perrakis, Juan C. Pizarro, Mark J. van Raaij, Theresa A. Ramelot, Francois Rousseau, Liang Tong, Amy K. Wernimont, Jasmine Young and Torsten Schwede

      Article first published online: 21 OCT 2011 | DOI: 10.1002/prot.23196

    2. CASP9 target classification (pages 21–36)

      Lisa N. Kinch, Shuoyong Shi, Hua Cheng, Qian Cong, Jimin Pei, Valerio Mariani, Torsten Schwede and Nick V. Grishin

      Article first published online: 14 OCT 2011 | DOI: 10.1002/prot.23190

  3. Template Based Assessment

    1. Top of page
    2. CASP Introduction—Round IX
    3. CASP Targets
    4. Template Based Assessment
    5. Free Modeling Assessment
    6. Refinement Assessment
    7. Assessment of Other Categories of Predictions
    8. Prediction Methods and Reports
    9. CASP Progress Reports
    1. Assessment of template based protein structure predictions in CASP9 (pages 37–58)

      Valerio Mariani, Florian Kiefer, Tobias Schmidt, Juergen Haas and Torsten Schwede

      Article first published online: 15 OCT 2011 | DOI: 10.1002/prot.23177

  4. Free Modeling Assessment

    1. Top of page
    2. CASP Introduction—Round IX
    3. CASP Targets
    4. Template Based Assessment
    5. Free Modeling Assessment
    6. Refinement Assessment
    7. Assessment of Other Categories of Predictions
    8. Prediction Methods and Reports
    9. CASP Progress Reports
    1. CASP9 assessment of free modeling target predictions (pages 59–73)

      Lisa Kinch, Shuo Yong Shi, Qian Cong, Hua Cheng, Yuxing Liao and Nick V. Grishin

      Article first published online: 14 OCT 2011 | DOI: 10.1002/prot.23181

  5. Refinement Assessment

    1. Top of page
    2. CASP Introduction—Round IX
    3. CASP Targets
    4. Template Based Assessment
    5. Free Modeling Assessment
    6. Refinement Assessment
    7. Assessment of Other Categories of Predictions
    8. Prediction Methods and Reports
    9. CASP Progress Reports
    1. Assessment of protein structure refinement in CASP9 (pages 74–90)

      Justin L. MacCallum, Alberto Pérez, Michael J. Schnieders, Lan Hua, Matthew P. Jacobson and Ken A. Dill

      Article first published online: 30 AUG 2011 | DOI: 10.1002/prot.23131

  6. Assessment of Other Categories of Predictions

    1. Top of page
    2. CASP Introduction—Round IX
    3. CASP Targets
    4. Template Based Assessment
    5. Free Modeling Assessment
    6. Refinement Assessment
    7. Assessment of Other Categories of Predictions
    8. Prediction Methods and Reports
    9. CASP Progress Reports
    1. Evaluation of model quality predictions in CASP9 (pages 91–106)

      Andriy Kryshtafovych, Krzysztof Fidelis and Anna Tramontano

      Article first published online: 14 OCT 2011 | DOI: 10.1002/prot.23180

    2. Evaluation of disorder predictions in CASP9 (pages 107–118)

      Bohdan Monastyrskyy, Krzysztof Fidelis, John Moult, Anna Tramontano and Andriy Kryshtafovych

      Article first published online: 16 SEP 2011 | DOI: 10.1002/prot.23161

    3. Evaluation of residue–residue contact predictions in CASP9 (pages 119–125)

      Bohdan Monastyrskyy, Krzysztof Fidelis, Anna Tramontano and Andriy Kryshtafovych

      Article first published online: 17 SEP 2011 | DOI: 10.1002/prot.23160

    4. Assessment of ligand-binding residue predictions in CASP9 (pages 126–136)

      Tobias Schmidt, Jürgen Haas, Tiziano Gallo Cassarino and Torsten Schwede

      Article first published online: 11 OCT 2011 | DOI: 10.1002/prot.23174

  7. Prediction Methods and Reports

    1. Top of page
    2. CASP Introduction—Round IX
    3. CASP Targets
    4. Template Based Assessment
    5. Free Modeling Assessment
    6. Refinement Assessment
    7. Assessment of Other Categories of Predictions
    8. Prediction Methods and Reports
    9. CASP Progress Reports
    1. Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method (pages 137–146)

      Liam J. McGuffin and Daniel B. Roche

      Article first published online: 30 AUG 2011 | DOI: 10.1002/prot.23120

    2. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement (pages 147–160)

      Dong Xu, Jian Zhang, Ambrish Roy and Yang Zhang

      Article first published online: 23 AUG 2011 | DOI: 10.1002/prot.23111

    3. Raptorx: Exploiting structure information for protein alignment by statistical inference (pages 161–171)

      Jian Peng and Jinbo Xu

      Article first published online: 11 OCT 2011 | DOI: 10.1002/prot.23175

    4. A multilayer evaluation approach for protein structure prediction and model quality assessment (pages 172–184)

      Jingfen Zhang, Qingguo Wang, Kittinun Vantasin, Jiong Zhang, Zhiquan He, Ioan Kosztin, Yi Shang and Dong Xu

      Article first published online: 14 OCT 2011 | DOI: 10.1002/prot.23184

    5. MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction (pages 185–195)

      Qingguo Wang, Kittinun Vantasin, Dong Xu and Yi Shang

      Article first published online: 14 OCT 2011 | DOI: 10.1002/prot.23185

  8. CASP Progress Reports

    1. Top of page
    2. CASP Introduction—Round IX
    3. CASP Targets
    4. Template Based Assessment
    5. Free Modeling Assessment
    6. Refinement Assessment
    7. Assessment of Other Categories of Predictions
    8. Prediction Methods and Reports
    9. CASP Progress Reports
    1. CASP9 results compared to those of previous casp experiments (pages 196–207)

      Andriy Kryshtafovych, Krzysztof Fidelis and John Moult

      Article first published online: 14 OCT 2011 | DOI: 10.1002/prot.23182

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