Structure-Based Phylogenetic Analysis

Question

[pixie@bioinfo]

We are interested to know some tools which can generate structure-based phylogenetic tree. We have already tried VMD which has an inbuilt program MultiSeq for this purpose, but we cannot do phylogenetic analysis for diverse structures with this tool.

Moreover, we are looking for a tool which can do phylogenetic analysis by considering any other criteria ( like TM score) other than RMSD.

Kindly help us on this...

Answer 1

[Khader Shameer]

Structure based phylogeny is a conceptual framework, not sure if there is any server/tool available for such analysis. There is a nice paper on structure based phylogeny using cupin fold from Molecular Biophysics Unit (NS Group and BG Lab).

Structure-Based Phylogeny as a Diagnostic for Functional Characterization of Proteins with a Cupin Fold. The article is available here.

This article explains the approach in a very detailed manner. They have used standard structural bioinformatics tools like JOY, DALI, SCOP along with ETA server and KITSCH from Phylip for the implementation of the method.

[pixie@bioinfo]

Thanx so much for the links..

[Arindam Ghosh]

Is there any tool to calculate SDM?

[Khader Shameer]

You can compute SDM as explained in the Methods section under: Evolutionary analysis using a structural divergence measure http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005736

Answer 2

[tanashri]

You can get Distance matrix of Q-score using PDBefold .and then use that distance matrix to calculate distance based phylogeny tree using MEGA(create .meg file of distance matrix.)