Proteins: Structure, Function, and Bioinformatics

Copyright © 2012 Wiley Periodicals Inc.

Cover image for Proteins: Structure, Function, and Bioinformatics

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

2003

Volume 53, Issue S6

Pages 333–595

  1. Editorial

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (page 333)

      Eaton E. Lattman

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10580

  2. Introductions

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Critical assessment of methods of protein structure prediction (CASP)-round V (pages 334–339)

      John Moult, Krzysztof Fidelis, Adam Zemla and Tim Hubbard

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10556

    2. CASP5 target classification (pages 340–351)

      Lisa N. Kinch, Yuan Qi, Tim J. P. Hubbard and Nick V. Grishin

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10555

  3. Comp. Modeling: Assessment

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Assessment of homology-based predictions in CASP5 (pages 352–368)

      Anna Tramontano and Veronica Morea

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10543

  4. Comp. Modelling: Prediction Reports

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. A “FRankenstein's monster” approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation (pages 369–379)

      Jan Kosinski, Iwona A. Cymerman, Marcin Feder, Michal A. Kurowski, Joanna M. Sasin and Janusz M. Bujnicki

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10545

    2. Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance (pages 380–388)

      Česlovas Venclovas

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10591

  5. Comp. Modeling: Prediction

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Modeling three-dimensional protein structures for CASP5 using the 3D-SHOTGUN meta-predictors (pages 389–394)

      Iris Sasson and Daniel Fischer

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10544

  6. Fold Recognition: Assessment

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. CASP5 assessment of fold recognition target predictions (pages 395–409)

      Lisa N. Kinch, James O. Wrabl, S. Sri Krishna, Indraneel Majumdar, Ruslan I. Sadreyev, Yuan Qi, Jimin Pei, Hua Cheng and Nick V. Grishin

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10557

  7. Fold Recognition: Prediction Reports

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment (pages 410–417)

      Krzysztof Ginalski and Leszek Rychlewski

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10548

    2. Application of 3D-Jury, GRDB, and Verify3D in fold recognition (pages 418–423)

      Marcin von Grotthuss, Jakub Pas, Lucjan Wyrwicz, Krzysztof Ginalski and Leszek Rychlewski

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10547

    3. Novel use of a genetic algorithm for protein structure prediction: Searching template and sequence alignment space (pages 424–429)

      Bruno Contreras-Moreira, Paul W. Fitzjohn, Marc Offman, Graham R. Smith and Paul A. Bates

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10549

    4. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling (pages 430–435)

      Donald Petrey, Zhexin Xiang, Christopher L. Tang, Lei Xie, Marina Gimpelev, Therese Mitros, Cinque S. Soto, Sharon Goldsmith-Fischman, Andrew Kernytsky, Avner Schlessinger, Ingrid Y.Y. Koh, Emil Alexov and Barry Honig

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10550

  8. New Fold Methods: Assessment

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Predictions without templates: New folds, secondary structure, and contacts in CASP5 (pages 436–456)

      Patrick Aloy, Alexander Stark, Caroline Hadley and Robert B. Russell

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10546

  9. New Fold Methods: Prediction Reports

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation (pages 457–468)

      Philip Bradley, Dylan Chivian, Jens Meiler, Kira M.S. Misura, Carol A. Rohl, William R. Schief, William J. Wedemeyer, Ora Schueler-Furman, Paul Murphy, Jack Schonbrun, Charles E.M. Strauss and David Baker

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10552

    2. TOUCHSTONE: A unified approach to protein structure prediction (pages 469–479)

      Jeffrey Skolnick, Yang Zhang, Adrian K. Arakaki, Andrzej Kolinski, Michal Boniecki, András Szilágyi and Daisuke Kihara

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10551

    3. Assembling novel protein folds from super-secondary structural fragments (pages 480–485)

      David T. Jones and Liam J. McGuffin

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10542

    4. Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments (pages 486–490)

      Qiaojun Fang and David Shortle

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10541

  10. New Fold Methods:Prediction Reports

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction (pages 491–496)

      Kevin Karplus, Rachel Karchin, Jenny Draper, Jonathan Casper, Yael Mandel-Gutfreund, Mark Diekhans and Richard Hughey

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10540

  11. New Fold Methods: Prediction Reports

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Predicting interresidue contacts using templates and pathways (pages 497–502)

      Yu Shao and Christopher Bystroff

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10539

  12. Predictions from Automatic Servers

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. CAFASP3: The third critical assessment of fully automated structure prediction methods (pages 503–516)

      Daniel Fischer, Leszek Rychlewski, Roland L. Dunbrack Jr., Angel R. Ortiz and Arne Elofsson

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10538

    2. 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3 (pages 517–523)

      Daniel Fischer

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10537

    3. Automated prediction of CASP-5 structures using the Robetta server (pages 524–533)

      Dylan Chivian, David E. Kim, Lars Malmström, Philip Bradley, Timothy Robertson, Paul Murphy, Charles E.M. Strauss, Richard Bonneau, Carol A. Rohl and David Baker

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10529

    4. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller (pages 534–541)

      Björn Wallner, Huisheng Fang and Arne Elofsson

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10536

    5. LiveBench-6: Large-scale automated evaluation of protein structure prediction servers (pages 542–547)

      Leszek Rychlewski, Daniel Fischer and Arne Elofsson

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10535

    6. CAFASP3 in the spotlight of EVA (pages 548–560)

      Volker A. Eyrich, Dariusz Przybylski, Ingrid Y.Y. Koh, Osvaldo Grana, Florencio Pazos, Alfonso Valencia and Burkhard Rost

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10534

  13. Prediction of Disorder

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Evaluation of disorder predictions in CASP5 (pages 561–565)

      Eugene Melamud and John Moult

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10533

    2. Predicting intrinsic disorder from amino acid sequence (pages 566–572)

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

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10532

    3. Prediction of disordered regions in proteins from position specific score matrices (pages 573–578)

      David T. Jones and Jonathan J. Ward

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10528

  14. New Methods

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Assessment of RAPTOR's linear programming approach in CAFASP3 (pages 579–584)

      Jinbo Xu and Ming Li

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10531

  15. Progress in Prediction Performance over Successive CASP Experiments

    1. Top of page
    2. Editorial
    3. Introductions
    4. Comp. Modeling: Assessment
    5. Comp. Modelling: Prediction Reports
    6. Comp. Modeling: Prediction
    7. Fold Recognition: Assessment
    8. Fold Recognition: Prediction Reports
    9. New Fold Methods: Assessment
    10. New Fold Methods: Prediction Reports
    11. New Fold Methods:Prediction Reports
    12. New Fold Methods: Prediction Reports
    13. Predictions from Automatic Servers
    14. Prediction of Disorder
    15. New Methods
    16. Progress in Prediction Performance over Successive CASP Experiments
    1. Assessment of progress over the CASP experiments (pages 585–595)

      C̆eslovas Venclovas, Adam Zemla, Krzysztof Fidelis and John Moult

      Article first published online: 15 OCT 2003 | DOI: 10.1002/prot.10530

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