Editing Structural bioinformatics (section)

=== Calculating contacts ===
Calculating contacts is an important task in structural bioinformatics, being important for the correct prediction of protein structure and folding, thermodynamic stability, protein-protein and protein-ligand interactions, docking and molecular dynamics analyses, and so on.<ref name=":0">{{Cite book| vauthors = Martins PM, Mayrink VD, de Silveira S, da Silveira CH, de Lima LH, de Melo-Minardi RC |title=Proceedings of the 33rd Annual ACM Symposium on Applied Computing |chapter=How to compute protein residue contacts more accurately? |date=2018|chapter-url=http://dl.acm.org/citation.cfm?doid=3167132.3167136|language=en|location=Pau, France|publisher=ACM Press|pages=60–67|doi=10.1145/3167132.3167136|isbn=978-1-4503-5191-1|s2cid=49562347}}</ref>

Traditionally, computational methods have used threshold distance between atoms (also called cutoff) to detect possible interactions.<ref>{{cite journal | vauthors = da Silveira CH, Pires DE, Minardi RC, Ribeiro C, Veloso CJ, Lopes JC, Meira W, Neshich G, Ramos CH, Habesch R, Santoro MM | display-authors = 6 | title = Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins | journal = Proteins | volume = 74 | issue = 3 | pages = 727–43 | date = February 2009 | pmid = 18704933 | doi = 10.1002/prot.22187 | s2cid = 1208256 | url = http://ainfo.cnptia.embrapa.br/digital/bitstream/item/147896/1/Proteins-Structure-Function-and-Bioinformatics.pdf }}</ref> This detection is performed based on Euclidean distance and angles between atoms of determined types. However, most of the methods based on simple Euclidean distance cannot detect occluded contacts. Hence, cutoff free methods, such as [[Delaunay triangulation]], have gained prominence in recent years. In addition, the combination of a set of criteria, for example, physicochemical properties, distance, geometry, and angles, have been used to improve the contact determination.<ref name=":0" /> 
{| class="wikitable"
|+Distance criteria for contact definition<ref name=":0" />
!Type
!Max distance criteria
|-
|Hydrogen bond
|3,9 Å
|-
|Hydrophobic interaction
|5 Å
|-
|Ionic interaction
|6 Å
|-
|Aromatic Stacking
|6 Å
|}