algorithm for suboptimal path calculations

[Former user]

Dear sir,

I did the suboptimal calculations

pa <- cnapath(net, from=32, to=135, k=500)

and i am fine with the results. But i didn't know the algorithm behind it. from your journal paper"Dynamic coupling and allosteric networks in the alpha subunit of heterotrimeric G proteins" i came to know about the Yen's algotihm for calculations of network path analysis. i tried to understand the algorithms but it is not happening.

so can you please provide some informations about the algorithm which BIO3D used for the path analysis in a simpler way for a better understanding.

thanking you in advance

[Xinqiu Yao]

Hi,

You don't have to read the Yen's algorithm paper to understand the function: As it's name indicated, the function calculates the sub-optimal paths, i.e. the shortest k paths, between two nodes. If you have no idea about 'path length', 'shortest path', etc., I may recommend read the paper by Sethi et al (PNAS 2009, 106:6620-6625), where some basic concepts of networks are defined.

Also, the paper by Van Wart et al (JCTC 2014, 10:511-517) gives another example application of sub-optimal path analysis, although their algorithm of searching the paths is different from ours (but the results are the same).