Editing CASP (section)

==Selection of target proteins==
In order to ensure that no predictor can have prior information about a protein's structure that would put them at an advantage, it is important that the experiment be conducted in a double-blind fashion: Neither predictors nor the organizers and assessors know the structures of the target proteins at the time when predictions are made. Targets for structure prediction are either structures soon-to-be solved by [[X-ray crystallography]] or NMR spectroscopy, or structures that have just been solved (mainly by one of the [[Protein Structure Initiative|structural genomics centers]]) and are kept on hold by the [[Protein Data Bank]]. If the given sequence is found to be related by common descent to a protein sequence of known structure (called a template), [[homology modeling|comparative protein modeling]] may be used to predict the [[tertiary structure]]. Templates can be found using [[sequence alignment]] methods (e.g. [[BLAST (biotechnology)|BLAST]] or [[HH-suite|HHsearch]]) or [[protein threading]] methods, which are better in finding distantly related templates. Otherwise, [[De novo protein structure prediction|''de novo'' protein structure prediction]] must be applied (e.g. Rosetta), which is much less reliable but can sometimes yield models with the correct fold (usually, for proteins less than 100-150 amino acids). Truly new folds are becoming quite rare among the targets,<ref>{{cite journal |vauthors=Tress ML, Ezkurdia I, Richardson JS |title=Target domain definition and classification in CASP8 |journal=Proteins |volume=77 Suppl 9 |issue=Suppl 9 |pages=10–7 |year=2009 |pmid=19603487 |pmc=2805415 |doi=10.1002/prot.22497}}</ref><ref name="zhang2005">{{cite journal |vauthors=Zhang Y, Skolnick J |title=The protein structure prediction problem could be solved using the current PDB library |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=102 |issue=4 |pages=1029–34 |date=January 2005 |pmid=15653774 |pmc=545829 |doi=10.1073/pnas.0407152101 |bibcode=2005PNAS..102.1029Z |doi-access=free}}</ref> making that category smaller than desirable.