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
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.
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.
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.
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.
Chothia, C. and Lesk, A. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J, 5(4), 823–826.
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.
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.
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.
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.
Eidhammer, I., Jonassen, I. and Taylor, W. R. (2005) Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis. Wiley & Sons, Chichester.
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.
Cozzetto, D. and Tramontano, A. (2005) Ten years of predictions,…,and counting. FEBS J, 272, 881–882.
Hubbard, T. J. (1999) RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions. Proteins, S3, 15–21.
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.
Zemla, A. (2003) LGA-a method for finding 3D similarities in protein structures. Nucleic Acids Res, 31, 3370– 3374.
Cozzetto, D. and Tramontano, A. (2005) Relationship between multiple sequence alignments and quality of protein comparative models. Proteins, 58(1), 151–157.
Valencia, A. (2005) Protein refinement: a new challenge for CASP in its 10th anniversary. Bioinformatics, 21(3), 277–277.
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.
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.
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.
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.
Tramontano, A., Leplae, R. and Morea, V. (2001) Analysis and assessment of comparative modeling predictions in CASP4. Proteins, S5, 22–38.
DeWeese-Scott, C. and Moult, J. (2004) Molecular modeling of protein function regions. Proteins, 55(4), 942–961.
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.
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.
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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
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