Open AccessLib ME —automatic extraction of 3D ligand‐binding motifs for mechanistic analysis of protein–ligand recognition
Author(s) -
He Wei,
Liang Zhi,
Teng MaiKun,
Niu LiWen
Publication year - 2016
Publication title -
febs open bio
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.718
H-Index - 31
ISSN - 2211-5463
DOI - 10.1002/2211-5463.12150
Subject(s) - ligand (biochemistry) , computational biology , structural motif , motif (music) , chemistry , binding site , protein ligand , sequence motif , extractor , biochemistry , biology , dna , receptor , physics , acoustics , process engineering , engineering
Identifying conserved binding motifs is an efficient way to study protein–ligand recognition. Most 3D binding motifs only contain information from the protein side, and so motifs that combine information from both protein and ligand sides are desired. Here, we propose an algorithm called Lib ME (Ligand‐binding Motif Extractor), which automatically extracts 3D binding motifs composed of the target ligand and surrounding conserved residues. We show that the motifs extracted by Lib ME for ATP and its analogs are highly similar to well‐known motifs reported by previous studies. The superiority of our method to handle flexible ligands was also demonstrated using isocitric acid as an example. Finally, we show that these motifs, together with their visual exhibition, permit better investigating and understanding of protein–ligand recognition process.