[Wish] protein contact maps

[goldbergtatyana]

The basic version would basically just be a matrix visualizer, but there are lots of nice visualization extensions possible like interactive highlighting, comparing two maps across the diagonal of the matrix, showing contacts in complexes, etc. A nice desktop viewer is CMView (http://www.bioinformatics.org/cmview/tutorial.html). We were thinking it could be a nice visualization feature in combination with a 3D viewer like ngl or iCn3D.

Spencer Bliven and Peter Rose

[sbliven]

While we're brainstorming features, contact maps are also closely related to the dot plots used for inspecting protein structure alignments (similar data matrix but different interpretation).

[josemduarte]

Just to let you know, we at RCSB PDB in San Diego have started working on the JS contact map viewer project. The idea is to be able to have bidirectional communication to a 3D viewer (NGL in our case). We are building the viewer using SVG and D3. I'll post in this issue with some links when there is some progress.

[josemduarte]

We have now made public the CMView.js repository. It has the basic functionality of displaying the map and communicating to the NGL 3D viewer bidirectionally. Multiple structures can also be shown by providing a multiple sequence alignment. Thanks to @garyyuya for doing a great job in implementing it!

[sbliven]

@josemduarte @garyyuya It would be great to add CMView to the BioJS repository