Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

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

2001

Volume 45, Issue S5

Pages 1–199

  1. Editor's Corner

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. CASP4 editorial (page 1)

      Eaton E. Lattman

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10061

  2. Introduction

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. Critical assessment of methods of protein structure prediction (CASP): Round IV (pages 2–7)

      John Moult, Krzysztof Fidelis, Adam Zemla and Tim Hubbard

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10054

    2. Prediction targets of CASP4 (pages 8–12)

      Alexey Murzin and Tim J.P. Hubbard

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10055

    3. Processing and evaluation of predictions in CASP4 (pages 13–21)

      Adam Zemla, Česlovas Venclovas, John Moult and Krzysztof Fidelis

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10052

  3. Comparative Modeling: Assessment

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. Analysis and assessment of comparative modeling predictions in CASP4 (pages 22–38)

      Anna Tramontano, Raphael Leplae and Veronica Morea

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10015

  4. Comparative Modeling: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM (pages 39–46)

      Paul A. Bates, Lawrence A. Kelley, Robert M. MacCallum and Michael J.E. Sternberg

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.1168

  5. Fold Recognition: Assessment

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. Assessment of the CASP4 fold recognition category (pages 55–67)

      Manfred J. Sippl, Peter Lackner, Francisco S. Domingues, Andreas Prlić, Rainer Malik, Antonina Andreeva and Markus Wiederstein

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10006

  6. Fold Recognition: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. Fold recognition from sequence comparisons (pages 68–75)

      Kristin K. Koretke, Robert B. Russell and Andrei N. Lupas

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10000

    2. What is the value added by human intervention in protein structure prediction? (pages 86–91)

      Kevin Karplus, Rachel Karchin, Christian Barrett, Spencer Tu, Melissa Cline, Mark Diekhans, Leslie Grate, Jonathan Casper and Richard Hughey

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10021

    3. Sequence-structure homology recognition by iterative alignment refinement and comparative modeling (pages 92–97)

      M.G. Williams, H. Shirai, J. Shi, H.G. Nagendra, J. Mueller, K. Mizuguchi, R.N. Miguel, S.C. Lovell, C.A. Innis, C.M. Deane, L. Chen, N. Campillo, D.F. Burke, T.L. Blundell and P.I.W. de Bakker

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.1169

  7. Ab Initio: Assessment

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
  8. Ab Initio: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. Rosetta in CASP4: Progress in ab initio protein structure prediction (pages 119–126)

      Richard Bonneau, Jerry Tsai, Ingo Ruczinski, Dylan Chivian, Carol Rohl, Charlie E. M. Strauss and David Baker

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.1170

    2. Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment (pages 133–139)

      Daron M. Standley, Volker A. Eyrich, Yuling An, David L. Pincus, John R. Gunn and Richard A. Friesner

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10005

    3. Application of PROSPECT in CASP4: Characterizing protein structures with new folds (pages 140–148)

      Dong Xu, Oakley H. Crawford, Philip F. LoCascio and Ying Xu

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10022

    4. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement (pages 149–156)

      Jeffrey Skolnick, Andrzej Kolinski, Daisuke Kihara, Marcos Betancourt, Piotr Rotkiewicz and Michal Boniecki

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.1172

    5. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations (pages 157–162)

      Piero Fariselli, Osvaldo Olmea, Alfonso Valencia and Rita Casadio

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.1173

  9. Comparison of Prediction Performance in Successive CASP4 Experiments

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. Comparison of performance in successive CASP experiments (pages 163–170)

      Česlovas Venclovas, Adam Zemla, Krzysztof Fidelis and John Moult

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10053

  10. Predictions in Automatic Servers

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. CAFASP2: The second critical assessment of fully automated structure prediction methods (pages 171–183)

      Daniel Fischer, Arne Elofsson, Leszek Rychlewski, Florencio Pazos, Alfonso Valencia, Burkhard Rost, Angel R. Ortiz and Roland L. Dunbrack Jr.

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10036

    2. LiveBench-2: Large-scale automated evaluation of protein structure prediction servers (pages 184–191)

      Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer and Leszek Rychlewski

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10039

  11. Predictions to Automatic Servers

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Comparative Modeling: Assessment
    5. Comparative Modeling: Prediction Reports
    6. Fold Recognition: Assessment
    7. Fold Recognition: Prediction Reports
    8. Ab Initio: Assessment
    9. Ab Initio: Prediction Reports
    10. Comparison of Prediction Performance in Successive CASP4 Experiments
    11. Predictions in Automatic Servers
    12. Predictions to Automatic Servers
    1. EVA: Large-scale analysis of secondary structure prediction (pages 192–199)

      Burkhard Rost and Volker A. Eyrich

      Version of Record online: 28 JAN 2002 | DOI: 10.1002/prot.10051

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