Proteins: Structure, Function, and Bioinformatics

Copyright © 2012 Wiley Periodicals Inc.

Cover image for Proteins: Structure, Function, and Bioinformatics

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

1999

Volume 37, Issue S3

Pages 1–237

  1. Editor's Corner

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Third meeting on the critical assessment of techniques for protein structure prediction (page 1)

      Eaton E. Lattman

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<1::AID-PROT1>3.0.CO;2-6

  2. Introduction

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Critical assessment of methods of protein structure prediction (CASP): Round III (pages 2–6)

      John Moult, Tim Hubbard, Krzysztof Fidelis and Jan T. Pedersen

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<2::AID-PROT2>3.0.CO;2-2

  3. Numerical Evaluation Methods

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Automated large scale evaluation of protein structure predictions (pages 7–14)

      Peter Lackner, Walter A. Koppensteiner, Francisco S. Domingues and Manfred J. Sippl

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<7::AID-PROT3>3.0.CO;2-V

    2. RMS/Coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions (pages 15–21)

      Tim J.P. Hubbard

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<15::AID-PROT4>3.0.CO;2-Z

    3. Processing and analysis of CASP3 protein structure predictions (pages 22–29)

      Adam Zemla, Česlovas Venclovas, John Moult and Krzysztof Fidelis

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W

  4. Comparative Modeling: Assessment

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. CASP3 comparative modeling evaluation (pages 30–46)

      T. Alwyn Jones and Gerard J. Kleywegt

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<30::AID-PROT6>3.0.CO;2-S

  5. Comparative Modeling: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Model building by comparison at CASP3: Using expert knowledge and computer automation (pages 47–54)

      Paul A. Bates and Michael J.E. Sternberg

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<47::AID-PROT7>3.0.CO;2-F

    2. An iterative structure-assisted approach to sequence alignment and comparative modeling (pages 55–60)

      David F. Burke, Charlotte M. Deane, Hampapathalu A. Nagarajaram, Nuria Campillo, Mercedes Martin-Martinez, Joaquim Mendes, Franck Molina, Jeff Perry, B.V.B. Reddy, Claudio M. Soares, Robert E. Steward, Mark Williams, Maria Armenia Carrondo, Tom L. Blundell and Kenji Mizuguchi

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B

  6. Comparative modeling: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Modeling three-dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence-derived predictions (pages 61–65)

      Daniel Fischer

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<61::AID-PROT9>3.0.CO;2-9

    2. Sequence to structure alignment in comparative modeling using PrISM (pages 66–72)

      An-Suei Yang and Barry Honig

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<66::AID-PROT10>3.0.CO;2-K

    3. Addressing the issue of sequence-to-structure alignments in comparative modeling of CASP3 target proteins (pages 73–80)

      Česlovas Venclovas, Krzysztof Ginalski and Krzysztof Fidelis

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<73::AID-PROT11>3.0.CO;2-P

  7. Comparative Modeling: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL (pages 81–87)

      Roland L. Dunbrack Jr.

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<81::AID-PROT12>3.0.CO;2-R

  8. Fold Recognition: Assessment

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Structure classification-based assessment of CASP3 predictions for the fold recognition targets (pages 88–103)

      Alexey G. Murzin

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<88::AID-PROT13>3.0.CO;2-3

  9. Fold Recognition: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure (pages 104–111)

      David T. Jones, Michael Tress, Kevin Bryson and Caroline Hadley

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<104::AID-PROT14>3.0.CO;2-P

    2. Sustained performance of knowledge-based potentials in fold recognition (pages 112–120)

      Francisco S. Domingues, Walter A. Koppensteiner, Markus Jaritz, Andreas Prlic, Christian Weichenberger, Markus Wiederstein, Hannes Floeckner, Peter Lackner and Manfred J. Sippl

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<112::AID-PROT15>3.0.CO;2-R

    3. Predicting protein structure using only sequence information (pages 121–125)

      Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate and Richard Hughey

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<121::AID-PROT16>3.0.CO;2-Q

    4. Cooperative approach for the protein fold recognition (pages 126–132)

      Motonori Ota, Takeshi Kawabata, Akira R. Kinjo and Ken Nishikawa

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<126::AID-PROT17>3.0.CO;2-8

    5. Threading with explicit models for evolutionary conservation of structure and sequence (pages 133–140)

      Anna Panchenko, Aron Marchler-Bauer and Stephen H. Bryant

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<133::AID-PROT18>3.0.CO;2-D

    6. Fold recognition using sequence and secondary structure information (pages 141–148)

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

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<141::AID-PROT19>3.0.CO;2-F

  10. Ab Initio: Assessment

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction (pages 149–170)

      C.A. Orengo, J.E. Bray, T. Hubbard, L. LoConte and I. Sillitoe

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<149::AID-PROT20>3.0.CO;2-H

  11. Ab Initio: Prediction Reports

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. Ab initio protein structure prediction of CASP III targets using ROSETTA (pages 171–176)

      Kim T. Simons, Rich Bonneau, Ingo Ruczinski and David Baker

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z

    2. Ab initio folding of proteins using restraints derived from evolutionary information (pages 177–185)

      Angel R. Ortiz, Andrzej Kolinski, Piotr Rotkiewicz, Bartosz Ilkowski and Jeffrey Skolnick

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<177::AID-PROT22>3.0.CO;2-E

    3. Improved ab Initio predictions with a simplified, flexible geometry model (pages 186–193)

      D.J. Osguthorpe

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<186::AID-PROT23>3.0.CO;2-D

    4. Ab initio protein structure prediction using a combined hierarchical approach (pages 194–198)

      Ram Samudrala, Yu Xia, Enoch Huang and Michael Levitt

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<194::AID-PROT24>3.0.CO;2-F

    5. Prediction of protein structure: The problem of fold multiplicity (pages 199–203)

      Andrei L. Lomize, Irina D. Pogozheva and Henry I. Mosberg

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<199::AID-PROT25>3.0.CO;2-Y

    6. Calculation of protein conformation by global optimization of a potential energy function (pages 204–208)

      Jooyoung Lee, Adam Liwo, Daniel R. Ripoll, Jaroslaw Pillardy and Harold A. Scheraga

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<204::AID-PROT26>3.0.CO;2-F

  12. Predictions From Automatic Servers

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. CAFASP-1: Critical assessment of fully automated structure prediction methods (pages 209–217)

      Daniel Fischer, Christian Barret, Kevin Bryson, Arne Elofsson, Adam Godzik, David Jones, Kevin J. Karplus, Lawrence A. Kelley, Robert M. MacCallum, Krzysztof Pawowski, Burkhard Rost, Leszek Rychlewski and Michael Sternberg

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<209::AID-PROT27>3.0.CO;2-Y

  13. Comparison of Prediction Quality in Three CASPS

    1. Top of page
    2. Editor's Corner
    3. Introduction
    4. Numerical Evaluation Methods
    5. Comparative Modeling: Assessment
    6. Comparative Modeling: Prediction Reports
    7. Comparative modeling: Prediction Reports
    8. Comparative Modeling: Prediction Reports
    9. Fold Recognition: Assessment
    10. Fold Recognition: Prediction Reports
    11. Ab Initio: Assessment
    12. Ab Initio: Prediction Reports
    13. Predictions From Automatic Servers
    14. Comparison of Prediction Quality in Three CASPS
    1. A measure of progress in fold recognition? (pages 218–225)

      Aron Marchler-Bauer and Stephen H. Bryant

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<218::AID-PROT28>3.0.CO;2-X

    2. An attempt to analyse progress in fold recognition from CASP1 to CASP3 (pages 226–230)

      Manfred J. Sippl, Peter Lackner, Francisco S. Domingues and Walter A. Koppensteiner

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<226::AID-PROT29>3.0.CO;2-Z

    3. Some measures of comparative performance in the three CASPs (pages 231–237)

      Česlovas Venclovas, Adam Zemla, Krzysztof Fidelis and John Moult

      Article first published online: 8 NOV 1999 | DOI: 10.1002/(SICI)1097-0134(1999)37:3+<231::AID-PROT30>3.0.CO;2-1

SEARCH

SEARCH BY CITATION