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Assessment of CASP8 structure predictions for template free targets
Author(s) -
BenDavid Moshe,
NoivirtBrik Orly,
Paz Aviv,
Prilusky Jaime,
Sussman Joel L.,
Levy Yaakov
Publication year - 2009
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/prot.22591
Subject(s) - casp , protein structure prediction , computer science , folding (dsp implementation) , computational biology , protein folding , rank (graph theory) , protein methods , artificial intelligence , protein structure , machine learning , bioinformatics , biology , peptide sequence , mathematics , engineering , genetics , biochemistry , gene , combinatorics , electrical engineering
The biennial CASP experiment is a crucial way to evaluate, in an unbiased way, the progress in predicting novel 3D protein structures. In this article, we assess the quality of prediction of template free models, that is, ab initio prediction of 3D structures of proteins based solely on the amino acid sequences, that is, proteins that did not have significant sequence identity to any protein in the Protein Data Bank. There were 13 targets in this category and 102 groups submitted predictions. Analysis was based on the GDT_TS analysis, which has been used in previous CASP experiments, together with a newly developed method, the OK_Rank, as well as by visual inspection. There is no doubt that in recent years many obstacles have been removed on the long and elusive way to deciphering the protein‐folding problem. Out of the 13 targets, six were predicted well by a number of groups. On the other hand, it must be stressed that for four targets, none of the models were judged to be satisfactory. Thus, for template free model prediction, as evaluated in this CASP, successes have been achieved for most targets; however, a great deal of research is still required, both in improving the existing methods and in development of new approaches. Proteins 2009. © 2009 Wiley‐Liss, Inc.