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Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

Fig 5

Iterative scheme for computing weights for templates by transforming the phylogenetic tree connecting them and the query protein into an equivalent tree with star-like topology with the query in the center.

(A) Templates t₁ and t₂ are closely related and should be down-weighted with respect to t₃. (B) Any tree with a structure at an internal node with unknown distance d_h to which all templates are connected in a star-like topology (top) can be transformed into an equivalent tree (bottom) with star-like topology, where equivalence means that the restraint on the distance d₀ of the top node is the same for both trees. τ₁, … τ_K indicate evolutionary distances. (C) Iterative restructuring of a phylogenetic tree. In each step, the basic transformation from Fig 5B is applied to the subtree colored in blue. Weights and edge lengths get updated until all templates are directly connected to the query.

doi: https://doi.org/10.1371/journal.pcbi.1004343.g005