Scaal: A Robust, Accurate, And High-efficient All-atomistic Protein Reconstruction Method From Low-resolution Protein Models

Abstract

In the quest to develop multiscale molecular simulation methods for complex protein dynamics that fuse high-resolution and low-resolution protein representations, it is important to investigate the required information of reconstruction of all-atomistic proteins from low resolution ones with manageable uncertainly. In this paper, we introduce a robust, accurate, and fast reconstruction method (SCAAL) that produces reliable all-atomistic protein structure by taking few beads from a coarse-grained model with at least one side chain bead and one Cα bead in the backbone (Side chain-Cα Model, SCM) into accounts. Our algorithm (SCAAL) is compared with SCWRL3.0 and it excels in robustness and is more accurate in the reconstruction of large amino acids. In addition, we further test SCAAL in the reconstruction of a complete protein folding trajectory from SCM coarse-grained models. We show that the efficiency, accuracy, and robustness of SCAAL as leverage for multi-scale simulations are excellent in terms of low root mean square deviations that lie within 1A resolution.