Computational protocol: CorNet: Assigning function to networks of co-evolving residues by automated literature mining

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Protocol publication

[…] The CMA network visualization tool was built using cytoscape.js (a JavaScript graph visualization library)[] and jquery (user interface libraries). In this HTML based network viewer nodes represent alignment positions (with the MSA position number indicated) and edges are coloured as function of the pairwise CMA values. The nodes are hyperlinked to underlying data stored in the database so that, for example, the amino acid distribution of an alignment position or a pair of correlating positions can be obtained rapidly.The user can interactively choose correlation cut-offs, colours for groups of residue positions, and residue positions can be coloured as function of their annotation. CorNet can write the resulting colours in a YASARA scene so that results can be visualised with YASARA, a protein structure visualisation tool (). When annotation queries are performed, the enrichment of the search term is determined on the fly. [...] 3DM was used to generate the structure bases multiple sequence alignments (MSAs) for the six super-families[]. In summary, structures are superposed with WHAT IF [] to generate an initial alignment that is then used to guide the alignment of all sequences for which no structure data is available. 3DM allows for the generation of alignments for subgroups of sequences. Such sub-alignments were generated for the UPD- and ADH protein families. These sub-alignments are composed of all sequences that have the most abundant residue at the position that forms the centre of the Network. Correlated mutation analysis is performed as described before[]. A method known as statistical coupling analysis[] is used to detect pairs of residues in the alignment that mutate simultaneously. […]

Pipeline specifications