Editing Protein (section)

===Structure prediction===

[[File:225 Peptide Bond-01.jpg|thumb|right|upright=1.6|Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing [[heme]] units]]

{{Main|Protein structure prediction|List of protein structure prediction software}}

Complementary to the field of structural genomics, ''protein structure prediction'' develops efficient [[mathematical model]]s of proteins to computationally predict the molecular formations in theory, instead of detecting structures with laboratory observation.<ref name=Zhang2008/> The most successful type of structure prediction, known as [[homology modeling]], relies on the existence of a "template" structure with sequence similarity to the protein being modeled; structural genomics' goal is to provide sufficient representation in solved structures to model most of those that remain.<ref name=Xiang2006/> Although producing accurate models remains a challenge when only distantly related template structures are available, it has been suggested that [[sequence alignment]] is the bottleneck in this process, as quite accurate models can be produced if a "perfect" sequence alignment is known.<ref name=Zhang2005/> Many structure prediction methods have served to inform the emerging field of [[protein engineering]], in which novel protein folds have already been designed.<ref name=Kuhlman2003/> Many proteins (in eukaryotes ~33%) contain large unstructured but biologically functional segments and can be classified as [[intrinsically disordered proteins]]. Predicting and analysing protein disorder is an important part of protein structure characterisation.<ref>{{cite journal | vauthors = Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT | title = Prediction and functional analysis of native disorder in proteins from the three kingdoms of life | journal = Journal of Molecular Biology | volume = 337 | issue = 3 | pages = 635–645 | date = March 2004 | pmid = 15019783 | doi = 10.1016/j.jmb.2004.02.002 | citeseerx = 10.1.1.120.5605 }}</ref>