Ordering Protein Contact Matrices.

ABSTRACT: Numerous biophysical approaches provide information about residues spatial proximity in proteins. However, correct assignment of the protein fold from this proximity information is not straightforward if the spatially close protein residues are not assigned to residues in the primary sequence. Here, we propose an algorithm to assign such residue numbers by ordering the columns and lines of the raw protein contact matrix directly obtained from proximity information between unassigned amino acids. The ordering problem is formatted as the search of a trail within a graph connecting protein residues through the nonzero contact values. The algorithm performs in two steps: (i) finding the longest trail of the graph using an original dynamic programming algorithm, (ii) clustering the individual o

SUBMITTER: Xu C 

PROVIDER: S-EPMC5889711 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature