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CASP2: Report on ab initio predictions
Author(s) -
Lesk Arthur M.
Publication year - 1997
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(1997)1+<151::aid-prot20>3.0.co;2-m
Subject(s) - ab initio , residue (chemistry) , protein secondary structure , protein structure prediction , computational chemistry , chemistry , crystallography , mathematics , statistical physics , computer science , physics , protein structure , organic chemistry , biochemistry
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 Q 3 ≥ 68 ( Q 3 = % 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. Proteins, Suppl. 1:151–166, 1997. © 1998 Wiley‐Liss, Inc.