Critical Assessment of Techniques for Protein Structure Prediction CASP

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). 

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

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. 

Two additional decoy data sets of misfolded proteins [17] and of predicted protein structures from the Critical Assessment of Techniques for Protein Stmcture Prediction (CASP) [67] are also used to illustrate the method and its utility. Individual components of the energy perform worse than the total energy for example, for the bulk of the well-packed decoys, the van der Waals energy provides very little information about structural similarity between a well-packed non-native structure and the native state. It is also shown that some aspects of the SGB model results can be mimicked by a screened electrostatic energy, although the SGB approximation provides a better discriminatory measure between non-native and native states. 

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. ... 

Various recently developed methods for ab initio protein structure predictions were tested during the CASP3 (Critical Assessment of Techniques for Protein Stmcture Prediction) exercises, concluded in December 1998 in Asilo-mar, California [127]. A number of new techniques have been developed before that time, and a number of them constitute qualitative progress in ab initio prediction with respect to the previous CASPs (held every two years). 

---