Protein Domain Boundary Predictions: A Structural Biology Perspective

Kirillova, Svetlana; Kumar, Suresh; Carugo, Oliviero

Several information about structure prediction methods are periodically published in the framework of the CASP *Address correspondence to this author at the Department of General Chemistry, Pavia University, Viale Taramelli 12, I-27100 Pavia, Italy; Tel: [phone]; E-mail: initiative, the main goal of which is to promote an evaluation of computational prediction methods [45] . This is a periodical exercise, performed every two years since 1994. During CASP experiment a series of protein sequences, the 3D structure of which was determined experimentally though it was not yet published, are distributed to research groups that develop computational methods for predicting protein structural features. It is thus a blinded test, where several methods of "in silico" structural biology techniques can be compared to the reality and to each other. Nevertheless, in each CASP run, the number of targets is obviously quite limited and a prediction method that performs very well in CASP is not necessarily better than other techniques in the reality. It is necessary to make additional investigations focusing on the possibility to use these prediction methods for practical application in structural biology.