Pathway Visualization Software Suggestions?
Entering edit mode
7.6 years ago
heronww • 0

I realize there's a tonne of other questions such as this, however I can't find any software or questions specifically addressing these two specific features I'm after -

1) I would like, in the pathways, to be able to click or hover over a molecule name and view the actual 2D chemical structure within the software program, as opposed to an external site. Or alternatively view the entire pathway with the molecular structures shown.

2) For each reaction step, to view the change in Gibbs free energy. This would be great.

Also, for the pathways themselves, could anyone recommend a database that shows all cofactors?

I installed PathVisio and imported pathways from wikipaths, however it seems none of the above features exist. Also, a lot of the cofactors seem to be missing (some steps don't show ADP -> ATP to exist). This isn't as pertinent as the two features mentioned above for the software that I'm looking for however.

Would anyone be able to recommend any software containing the above two features, and a pathway database that doesn't fail to omit key steps such as ADP -> ATP, or NAD+ -> NADH conversion like wikipaths seems to do?


pathway-software • 1.3k views
Entering edit mode

Something like that is what I'm looking for, thanks Zhilong. Although I can't seem to zoom out to view the pathway in a reasonable level without it becoming unreadable.

Entering edit mode
7.6 years ago
Zhilong Jia ★ 2.1k

A recent published tool, Pathwhiz, can partly cope with your problem (at least the first one).

ref. Pathways with PathWhiz


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