From fold recognition to homology modeling: an analysis of protein modeling challenges at different levels of...

An analysis of different approaches to protein structure prediction is presented based solely on the range of models submitted to the third Critical Assessment of Protein Structure Prediction (CASP3) conference. CASP conferences evaluate the current state of the art of protein structure prediction by comparing blind prediction efforts of many groups for the same set of target sequences. Target sequences may be highly similar to those with known structure or can be totally (at least superficially) sequentially dissimilar. Techniques applied to those blind predictions (over 40 targets) ranges from a detailed homology prediction to the detection of remote homologues well below a twilight zone of protein sequence similarity. For the CASP3 conference, we have submitted predictions, totaling 35, with various levels of difficulty and complexity. For ten submitted homology targets, eight of them were determined by experiment so far. The RMSD of C-alpha atoms are 1.2-1.7, 2.3, and 4.6-17.9 A for the three easy targets, two hard targets, and three very hard homology targets, respectively. Out of 18-fold recognition predictions available for analysis, we got six correct predictions, five near misses, three tough near misses and four far misses. Here we analyze successes and failures of those predictions in an attempt to identify common problems and common achievements.