CASP2: report on ab initio predictions.

Submissions in the ab initio category included predictions of secondary structure, three-dimensional coordinate sets, modes of oligomerization, and residue and secondary structure segment contact patterns. For secondary structure prediction, four groups showed sustained success according the the criterion Q3 > or = 68 (Q3 = % of residues correctly assigned to the categories helix, strand, and other). The best program, Rost's PHD, scored over this threshold in 13 of its 16 assessable attempts. For the prediction of full three-dimensional coordinates, no group could claim sustained success in prediction of generally correct structures over a range of targets. However, satisfactory predictions were achieved in one case, pig NK-lysin (target 42), a 78-residue protein with three disulfide bridges. For the prediction of contacts, Olmea, Pazos, and Valencia have developed specialized methods for residue-residue proximity patterns, and Gerloff, Joachimiak, Cohen, and Benner for segment contacts.