Editing Protein structure prediction (section)

===Before modelling===
Most tertiary structure modelling methods, such as Rosetta, are optimized for modelling the tertiary structure of single protein domains. A step called '''domain parsing''', or '''domain boundary prediction''', is usually done first to split a protein into potential structural domains. As with the rest of tertiary structure prediction, this can be done comparatively from known structures<ref>{{cite journal |vauthors=Ovchinnikov S, Kim DE, Wang RY, Liu Y, DiMaio F, Baker D |title=Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta |journal=Proteins |volume=84 |pages=67–75 |date=September 2016 |issue=Suppl 1 |pmid=26677056 |doi=10.1002/prot.24974 |pmc=5490371}}</ref> or ''ab initio'' with the sequence only (usually by [[machine learning]], assisted by covariation).<ref>{{cite journal |vauthors=Hong SH, Joo K, Lee J |title=ConDo: Protein domain boundary prediction using coevolutionary information |journal=Bioinformatics |volume=35 |issue=14 |pages=2411–2417 |date=November 2018 |pmid=30500873 |doi=10.1093/bioinformatics/bty973}}</ref> The structures for individual domains are docked together in a process called '''domain assembly''' to form the final tertiary structure.<ref>{{cite journal |vauthors=Wollacott AM, Zanghellini A, Murphy P, Baker D |title=Prediction of structures of multidomain proteins from structures of the individual domains |journal=Protein Science |volume=16 |issue=2 |pages=165–75 |date=February 2007 |pmid=17189483 |doi=10.1110/ps.062270707 |pmc=2203296}}</ref><ref>{{cite journal |vauthors=Xu D, Jaroszewski L, Li Z, Godzik A |title=AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction |journal=Bioinformatics |volume=31 |issue=13 |pages=2098–105 |date=July 2015 |pmid=25701568 |doi=10.1093/bioinformatics/btv092 |pmc=4481839}}</ref>