Editing Bioinformatics (section)

===Molecular interaction networks===
{{main|Protein–protein interaction prediction|interactome}}
[[File:The protein interaction network of Treponema pallidum.png|200px|thumbnail|right|Interactions between proteins are frequently visualized and analyzed using networks. This network is made up of protein–protein interactions from ''[[Treponema pallidum]]'', the causative agent of [[syphilis]] and other diseases.<ref>{{cite journal | vauthors = Titz B, Rajagopala SV, Goll J, Häuser R, McKevitt MT, Palzkill T, Uetz P | title = The binary protein interactome of Treponema pallidum--the syphilis spirochete | journal = PLOS ONE | volume = 3 | issue = 5 | pages = e2292 | date = May 2008 | pmid = 18509523 | pmc = 2386257 | doi = 10.1371/journal.pone.0002292 | bibcode = 2008PLoSO...3.2292T | veditors = Hall N | doi-access = free }}</ref>]]

Tens of thousands of three-dimensional protein structures have been determined by [[X-ray crystallography]] and [[protein nuclear magnetic resonance spectroscopy]] (protein NMR) and a central question in structural bioinformatics is whether it is practical to predict possible protein–protein interactions only based on these 3D shapes, without performing [[protein–protein interaction]] experiments. A variety of methods have been developed to tackle the [[protein–protein docking]] problem, though it seems that there is still much work to be done in this field.

Other interactions encountered in the field include Protein–ligand (including drug) and [[protein–peptide]]. Molecular dynamic simulation of movement of atoms about rotatable bonds is the fundamental principle behind computational [[algorithm]]s, termed docking algorithms, for studying [[interactome|molecular interactions]].