Atomistic Structure Prediction from Coarse-Grained Peptide using Conformation Database

Abstract

Coarse-grained models improve the computational efficiency and allow calculations in a wide range and long timescale for macromolecular systems. Although, detail information of the all-atom models is often required along with the efficiency of coarse-grained models. Because our docking method using coarse-grained models predicts the binding site as a Cα structure, it is necessary to transform the coarse-grained model into the all-atom model for high accuracy analyses. In this work, we propose a new CBRM (Conformation-based Reverse Mapping) method that constructs the all-atom geometry from a coarse-grained peptide in a binding site. In order to address a huge variety of geometry of the peptide in a binding site of complex structure, we create the complete tripeptide conformation DB by exhaustive conformation search and use them as templates of the all-atom structure. By combining the conformation DB, CBRM method can construct the all-atom structure for a coarse-grained peptide of arbitrary residue length. In addition, we considered new coarse-grained models that improve the accuracy of the all-atom model construction of CBRM method.