Editing Structural bioinformatics (section)

=== Structure validation ===
After structure modeling, an additional step of structure validation is necessary since many of both comparative and 'de novo' modeling algorithms and tools use [[heuristic]]s to try assembly the 3D structure, which can generate many errors. Some validation strategies consist of calculating energy scores and comparing them with experimentally determined structures. For example, the [[Discrete optimized protein energy|DOPE score]] is an energy score used by the [[MODELLER|MODELLER tool]] for determining the best model.<ref>{{cite journal | vauthors = Webb B, Sali A | title = Comparative Protein Structure Modeling Using MODELLER | journal = Current Protocols in Bioinformatics | volume = 47 | issue = 1 | pages = 5.6.1–32 | date = September 2014 | pmid = 25199792 | doi = 10.1002/0471250953.bi0506s47 | pmc = 4186674 }}</ref>

Another validation strategy is calculating φ and ψ backbone dihedral angles of all residues and construct a [[Ramachandran plot]]. The side-chain of [[amino acid]]s and the nature of interactions in the backbone restrict these two angles, and thus, the visualization of allowed conformations could be performed based on the [[Ramachandran plot]]. A high quantity of amino acids allocated in no permissive positions of the chart is an indication of a low-quality modeling.