id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-103869-ii6qi1bp	Yang, Liu	Defining a Global Map of Functional Group Based 3D Ligand-binding Motifs	2020-09-28		.txt	text/plain	7435	386	51	Current methods based on structural comparison or alignment of protein pockets have identified many well-defined 3D motifs that are conserved across different protein pockets and widely used for protein function annotation, pockets classification and ligand-binding prediction (Gao and Skolnick, 2013; Hoffmann et al., 2010; Hwang et al., 2017; Pires et al., 2013; Pu et al., 2019; Yeturu and Chandra, 2008) . To systematically identify and evaluate 3D binding motifs at FG level, we developed AFTME, an alignment-free method that automatically maps functional atoms to different FGs from a set of protein pockets binding the same ligand using two-dimensional clustering approach. We have developed AFTME, a computational method to dissect protein pockets binding a specific ligand into sectors that interact with different functional groups (FGs). The basic assumption of this method is simple: if conserved binding pattern for a specific FG exists, the pattern-forming atoms should be spatially proximal to the corresponding FG and frequently co-appear, thus can be detected through clustering analysis of functional atoms from diverse protein pockets binding the same ligand.	./cache/cord-103869-ii6qi1bp.txt	./txt/cord-103869-ii6qi1bp.txt