GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.

ABSTRACT: Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applic

SUBMITTER: Kinjo AR 

PROVIDER: S-EPMC4629647 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature