title: LibME-automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein-ligand recognition.
abstract: 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 LibME (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 LibME 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.
authors.affiliation: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China.
authors.forename: Wei
authors.initials: W
authors.lastname: He
authors.affiliation: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Liang
authors.affiliation: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China.
authors.forename: MaiKun
authors.initials: M
authors.lastname: Teng
authors.affiliation: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China.
authors.forename: LiWen
authors.initials: L
authors.lastname: Niu
keywords: algorithm; binding motif; protein–ligand recognition