Structure prediction assessment

MJE Sternberg, PA Bates, LA Kelley, RM MacCallum. Progress m protein structure prediction Assessment of CASP3. Curr Opm Struct Biol 9 368-373, 1999. 

A. Zemia, C. Venclovas, K. Fidelis, B. Rost. A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment. Proteins. 1999, 34, 220-223. 

Sternberg, M.J., Bates, P.A., Kelley, L.A. and MacCallum, R.M. (1999) Progress in protein structure prediction assessment of CASP3. Curr. Opin. Struct. Biol. 9 368-373. 

CASP stands for Critical Assessment of techniques for protein Structure Prediction. 

Moult J, T Hubbard, K Fldelis and J T Pedersen 1999. Critical Assessment of Methods of Protein Structure Prediction (CASP) Round III. Proteins Structure, Function and Genetics Suppl. 3 2-6. 

J Moult, T Flubbard, SFI Bryant, K Fidelis, JT Pedersen. Critical assessment of methods of protein structure prediction (CASP) Round II. Proteins Suppl 1 2-6, 1997. 

RL Dunbrack Jr, DL Gerloff, M Bower, X Chen, O Lichtarge, FE Cohen. Meeting review The second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar, CA, Dec 13-16, 1996. Folding Des 2 R27-R42, 1997. 

During this process of designing sequence changes, models were built and assessed to ensure that there were no obvious steric clashes and that the hydrophobic core was well packed. Furthermore, secondary structure prediction was also used to monitor the progress of change and to choose among different possible substitutions. The final sequence (see Table 17.3) contains 28 changes it had 50% identity to B1 and the similarity to Rop had increased from 5.4% identity to 41%. 

The strongest verification for a 3D-protein model comes from the experimental 3D-structure. This is the objective of the Critical Assessment of Techniques for Protein Structure Prediction, CASP ( http //predic tioncenter.org), where the structural models are made in advance of the experimental structure of a particular protein. 

Chasman, D. and R.M. Adams, "Predicting the Functional Consequences of Non-Synonymous Single Nucleotide Polymorphisms Structure-Based Assessment of Amino Acid Variation," /. Mol. Biol., 307, 683-706 (2001). 

CASP (Critical Assessment on Structure Prediction) 89 catalysis 55,66... 

As the above results show, the gross features of the cellulose I crystal structure predicted by various methods do not differ appreciably, but the accompanying deviations in the R -factors are significant. When these predictions are used to assess, for example, whether the cellulose I crystal structure is based on parallel- or antmarallel-chains, the range in the R"-factors seen for the parallel models (cf. Table II) is comparable to that between the two different polarity models. As shown in Fig. 5, the most probable parallel- and antiparallel-chain structures of cellulose I, refined by minimizing the function O, differ in R -factors by approximately the same extent as the three predictions for the parallel model shown in Fig. 4 and Table II. 

D Fischer, C Barret, K Bryson, A Elofsson, A Godzik, D Jones, KJ Karplus, LA Kelley, RM MacCallum, K Pawowski, B Rost, L Rychlewski, MJ Sternberg. CA-FASP-1 critical assessment of fully automated structure prediction methods. Proteins Structure, Function and Genetics (Suppl) 3 209-217, 1999. 

Daniel Chasman R, Adams M. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms structure-based assessment of amino acid variation. J Mol Biol 1996 307 683-706. 

Protein-structure prediction methods are routinely compared and contrasted in a public competition called the Critical Assessment of Techniques for Protein Structure Prediction (CASP). These large-scale events allow for a comparison of the state-of-the-art tools and algorithms on a variety of target sequences. The results of each event are scrutinized. There have been five such events thus far, with CASP5 being the most recent (31). 

The REFINER model had been tested in the CASP5 (every second year community-wide Critical Assessment of Techniques for Protein Structure Prediction) experiment and in a benchmark of de novo prediction of protein fragments. Both tests have shown better performance than that achieved by standard molecular modeling tools. During the next round, CASP6 of the protein structure prediction, the REFINER model produced several very good predictions, especially in the new fold category. 

Source Data from Liljas A, Rossmann MG. X-ray studies of protein interactions. Annu Rev Biochem 43 475-505, 1974 Argos P, Schwarz JS, Schwarz J. An assessment of protein secondary structure prediction methods based on amino acid sequence. Biochim Biophys Acta 439 261-273, 1976. 

Abstract Methods, evolutionary and systematic search approaches, and applications of crystal structure prediction of closest-packed and framework materials are reviewed. Strategies include developing better cost functions, used to assess the quality of the candidate structures that are generated, and ways to reduce the set of candidate structures to be assessed. The crystallographic coordinates for new materials, available only as a powder sample, are often intractable from diffraction data alone. In recent years, steady progress has been made in the ability to solve previously unknown crystal structures of such compounds, the generation of known structures (inferring more confidence in such approaches) and the prediction of hypothetical yet-to-be-synthesised structures. 

CASP Critical assessment of methods of protein structure prediction... 

---