Editing Protein structure (section)

==Structural classifications of proteins==
Protein structures can be grouped based on their structural similarity, [[circuit topology|topological class]] or a common [[evolution]]ary origin. The [[Structural Classification of Proteins database]]<ref name="pmid7723011">{{cite journal | vauthors = Murzin AG, Brenner SE, Hubbard T, Chothia C | title = SCOP: a structural classification of proteins database for the investigation of sequences and structures | journal = Journal of Molecular Biology | volume = 247 | issue = 4 | pages = 536–540 | date = April 1995 | pmid = 7723011 | doi = 10.1016/S0022-2836(05)80134-2 | url = http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf | url-status = dead | archive-date = 26 April 2012 | df = dmy-all | archive-url = https://web.archive.org/web/20120426170732/http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf | author-link4 = Cyrus Chothia | author-link2 = Steven E. Brenner | author-link3 = Tim Hubbard }}</ref> and [[CATH]] database<ref name="pmid9309224">{{cite journal | vauthors = Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM | title = CATH--a hierarchic classification of protein domain structures | journal = Structure | volume = 5 | issue = 8 | pages = 1093–1108 | date = August 1997 | pmid = 9309224 | doi = 10.1016/S0969-2126(97)00260-8 | doi-access = free | author-link6 = Janet Thornton | author-link1 = Christine Orengo }}</ref> provide two different structural classifications of proteins. When the structural similarity is large the two proteins have possibly diverged from a common ancestor,<ref name="Pascual2009">{{cite journal | vauthors = Pascual-García A, Abia D, Ortiz AR, Bastolla U | title = Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures | journal = PLOS Computational Biology | volume = 5 | issue = 3 | pages = e1000331 | date = March 2009 | pmid = 19325884 | pmc = 2654728 | doi = 10.1371/journal.pcbi.1000331 | bibcode = 2009PLSCB...5E0331P | doi-access = free }}</ref> and shared structure between proteins is considered evidence of  [[Homology (biology)|homology]]. Structure similarity can then be used to group proteins together into [[protein superfamilies]].<ref>{{cite journal | vauthors = Holm L, Rosenström P | title = Dali server: conservation mapping in 3D | journal = Nucleic Acids Research | volume = 38 | issue = Web Server issue | pages = W545–W549 | date = July 2010 | pmid = 20457744 | pmc = 2896194 | doi = 10.1093/nar/gkq366 }}</ref> If shared structure is significant but the fraction shared is small, the fragment shared may be the consequence of a more dramatic evolutionary event such as [[horizontal gene transfer]], and joining proteins sharing these fragments into protein superfamilies is no longer justified.<ref name="Pascual2009"></ref> Topology of a protein can be used to classify proteins as well. [[Knot theory]] and [[circuit topology]] are two topology frameworks developed for classification of protein folds based on chain crossing and intrachain contacts respectively.