Critical Assessment of Techniques for Protein Structure Prediction

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

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. 

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. 

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-... 

The number of atoms taken into account in MD nowadays may reach a million. The real problem is not the size of the system, but rather its complexity and the wealth of possible structures, with their too large number to be investigated. Some problems may be simplified by considering a quantum-mechanical part in the details and a classical part described by Newton equations. Another important problem is to predict the 3-D structure of proteins, starting from the available amino acid sequence. Every two years beginning in 1994, CASP (Critical Assessment of techniques for protein Structure Prediction) has been organized in California. CASP is a kind of scientific competition, in which theoretical laboratories (knowing only the amino acid sequence) make blind predictions about 3-D protein structures about to be determined in experimental laboratories. Most of the theoretical methods are based on the similarity of the sequence to a sequence from the Protein Data Bank of the 3-D structures, only some of the methods are related to chemical physics. Fig. 7.17 shows an example of the latter. 

Critical Assessment of Techniques for Protein Structure Prediction, Protein Structure Pre-... 

The UNRES model represents one of the most accurate CG force fields for protein folding, as confirmed by several assessments at CASP (Critical Assessment of Techniques for Protein Structure Prediction).Recently the UNRES model proved to have good reliability also in predicting protein oligomerisation. ... 

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