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The Assessment of Methods for Protein Structure Prediction

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Protein Structure Prediction

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 413))

Summary

Methods for protein structure prediction are flourishing and becoming widely available to both experimentalists and computational biologists. But, how good are they? What is their range of applicability and how can we know which method is better suited for the task at hand? These are the questions that this chapter tries to address, by describing automatic evaluation methods as well as the world-wide Critical Assessment of Techniques for Protein Structure Prediction (CASP) initiative and focusing on the specific problems of assessing the quality of a protein 3D model.

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References

  1. Browne, W. J., North, A. C., Phillips, D. C., Brew, K., Vanaman, T. C. and Hill, R. L. (1969) A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen’s egg-white lysozyme. J Mol Biol, 42, 65–86.

    Article  CAS  PubMed  Google Scholar 

  2. Moult, J., Pedersen, J., Judson, R. and Fidelis, K. (1995) A large-scale experiment to assess protein structure prediction methods. Proteins, 23(3), ii–v.

    Article  CAS  PubMed  Google Scholar 

  3. Koh, I. Y., Eyrich, V. A., Marti-Renom, M. A., Przybylski, D., Madhusudhan, M. S., Eswar, N., Grana, O., Pazos, F., Valencia, A., Sali, A., et al. (2003) EVA: evaluation of protein structure prediction servers. Nucleic Acids Res, 31(13), 3311–3315.

    Article  CAS  PubMed  Google Scholar 

  4. Fischer, D., Elofsson, A. and Rychlewski, L. (2000) The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-a-vis human teams in the protein structure prediction experiment CAFASP2. Protein Eng, 13(10), 667– 670.

    Article  CAS  PubMed  Google Scholar 

  5. Chothia, C. and Lesk, A. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J, 5(4), 823–826.

    CAS  PubMed  Google Scholar 

  6. Sippl, M. J. and Weitckus, S. (1992) Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins, 13(3), 258–271.

    Article  CAS  PubMed  Google Scholar 

  7. Gribskov, M., McLachlan, A. D. and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci USA, 84(13), 4355–4358.

    Article  CAS  PubMed  Google Scholar 

  8. Simons, K. T., Bonneau, R., Ruczinski, I. and Baker, D. (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins, S3, 171–176.

    Article  Google Scholar 

  9. Bayley, M. J., Jones, G., Willett, P. and Williamson, M. P. (1998) GENFOLD: a genetic algorithm for folding protein structures using NMR restraints. Protein Sci, 7(2), 491–499.

    Article  CAS  PubMed  Google Scholar 

  10. Eidhammer, I., Jonassen, I. and Taylor, W. R. (2005) Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis. Wiley & Sons, Chichester.

    Google Scholar 

  11. Kryshtafovych, A., Milostan, M., Szajkowski, L., Daniluk, D. and Fidelis, K. (2005) CASP6 data processing and automatic evaluation at the protein structure prediction center. Proteins, S7, 19–23.

    Article  Google Scholar 

  12. Cozzetto, D. and Tramontano, A. (2005) Ten years of predictions,…,and counting. FEBS J, 272, 881–882.

    Article  CAS  PubMed  Google Scholar 

  13. Hubbard, T. J. (1999) RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions. Proteins, S3, 15–21.

    Article  Google Scholar 

  14. Moult, J., Fidelis, K., Rost, B., Hubbard, T. and Tramontano, A. (2005) Critical assessment of methods of protein structure prediction (CASP) - round 6. Proteins, S7, 3–7.

    Article  Google Scholar 

  15. Zemla, A. (2003) LGA-a method for finding 3D similarities in protein structures. Nucleic Acids Res, 31, 3370– 3374.

    Article  CAS  PubMed  Google Scholar 

  16. Cozzetto, D. and Tramontano, A. (2005) Relationship between multiple sequence alignments and quality of protein comparative models. Proteins, 58(1), 151–157.

    Article  CAS  PubMed  Google Scholar 

  17. Valencia, A. (2005) Protein refinement: a new challenge for CASP in its 10th anniversary. Bioinformatics, 21(3), 277–277.

    Article  CAS  PubMed  Google Scholar 

  18. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res, 28(1), 235–242.

    Article  CAS  PubMed  Google Scholar 

  19. Bujnicki, J. M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) LiveBench-1: continuous benchmarking of protein structure prediction servers. Protein Sci, 10(2), 352–361.

    Article  CAS  PubMed  Google Scholar 

  20. Fischer, D., Elofsson, A., Rychlewski, L., Pazos, F., Valencia, A., Rost, B., Ortiz, A. R. and Dunbrack R. L. Jr. (2001) CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins, S5, 171–183.

    Article  Google Scholar 

  21. Chothia, C., Lesk, A. M., Tramontano, A., Levitt, M., Smith Gill, S. J., Air, G., Sheriff, S., Padlan, E. A., Davies, D. and Tulip, W. R. (1989) Conformations of immunoglobulin hypervariable regions. Nature, 342(6252), 877–883.

    Article  CAS  PubMed  Google Scholar 

  22. Tramontano, A., Leplae, R. and Morea, V. (2001) Analysis and assessment of comparative modeling predictions in CASP4. Proteins, S5, 22–38.

    Article  Google Scholar 

  23. DeWeese-Scott, C. and Moult, J. (2004) Molecular modeling of protein function regions. Proteins, 55(4), 942–961.

    Article  CAS  PubMed  Google Scholar 

  24. Pizzi, E., Tramontano, A., Tomei, L., La Monica, N., Failla, C., Sardana, M., Wood, T. and De Francesco, R. (1994) Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. Proc Natl Acad Sci USA, 91(3), 888–892.

    Google Scholar 

  25. Giorgetti, A., Raimondo, D., Miele, A. E. and Tramontano, A. (2005) Evaluating the usefulness of protein structure models for molecular replacement. Bioinformatics, 21(2), ii72–ii76.

    Article  CAS  PubMed  Google Scholar 

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© 2008 Humana Press Inc

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Tramontano, A., Cozzetto, D., Giorgetti, A., Raimondo, D. (2008). The Assessment of Methods for Protein Structure Prediction. In: Zaki, M.J., Bystroff, C. (eds) Protein Structure Prediction. Methods in Molecular Biology™, vol 413. Humana Press. https://doi.org/10.1007/978-1-59745-574-9_2

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  • DOI: https://doi.org/10.1007/978-1-59745-574-9_2

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-752-5

  • Online ISBN: 978-1-59745-574-9

  • eBook Packages: Springer Protocols

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