GR-Align (GRaphlet-based Aligner) is a fast heuristic procedure for aligning/comparing protein structures according to the Contact Map Opverlap maximization (CMO) paradigm. The algorithm is based on a Needleman-Wunch algorithm where the cost for matching two residues is their graphlet degree similarity.
GR-Align packages contains three software: CMap, DCount, and GR-Align:
CMap converts protein structures (.pdb) files into contact map graphs (leda graphs .gw)
DCount computes the graphlet degree signatures (.ndump files) from Contact Maps
GR-Align aligns protein structures (requieres both contact maps and signatures files)
:: MORE INFORMATION
Bioinformatics. 2014 May 1;30(9):1259-65. doi: 10.1093/bioinformatics/btu020. Epub 2014 Jan 17.
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.
Malod-Dognin N1, Pržulj N.