Critical Assessment of Structure Prediction

Noble MEM, Verlinde CLMJ, Groendijk H, Kalk KH, Wierenga RK, Hoi WGJ. Crystallographic and molecular modeling studies on trypanosomal triosephosphate isomerase a critical assessment of the predicted and observed structures of the complex with 2-phospho-glycerate. J Med Chem 1991 34 2709-2718. 

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. 

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. 

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. 

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. 

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

Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tra-montano A. Critical assessment of methods of protein structure prediction-Round Vll. Proteins. 2007 69 3-9. 

Neural Networks. PROBE (376) is an integrated suite of neural network modules that predicts folding motif, secondary structure per residue, location of disulfide bonds, and surface accessibility of each residue. No critical assessment of the accuracy of the results from this package was given in the description, but is available for evaluation. 

Currently, methods of structure prediction from sequence perform poorly. The results of the biannual CASP experiment (Critical Assessment of techniques for protein Structure Prediction see http //predictioncenter.llnl. gov/) are equivocal to say the least. A recent report on the improvements of aligning target sequences to a structural template (67) indicates that over the last four CASP competitions there was no significant improvement in quality in this key step in the prediction process. Alignment remains the major source of error in all models based on less than 30% se-... 

Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, et al. CAFASP-1 Critical assessment of fully automated structure prediction methods. Proteins 1999 37(Suppl 3) 209-17. 

Fischer D, Rychlewski L, Dunbrack RL, Jr., Ortiz AR, Elofsson A. CAFASP3 The third critical assessment of fully automated structure prediction methods. Proteins 2003 53(Suppl 6) 503-16. 

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