One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model

TL;DR

The paper discusses the CABS coarse-grained protein model, which simplifies protein structures to improve computational efficiency, using one-dimensional structural properties and knowledge-based force fields for various modeling applications.

Contribution

It introduces the CABS model's unique design based on 1D structural properties and details its applications in protein structure prediction and dynamics modeling.

Findings

CABS model effectively captures protein secondary structures.

The model enables efficient multiscale protein simulations.

Tools are freely available for diverse protein modeling tasks.

Abstract

Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps the most successful strategy to overcome the inefficiency problem is multiscale modeling to merge all-atom and coarse-grained models. This chapter describes a well-established CABS coarse-grained protein model. The CABS (C-Alpha, C-Beta and Side chains) model assumes a 2-4 united-atom representation of amino acids, knowledge-based force field (derived from the statistical regularities seen in known protein sequences and structures) and efficient Monte Carlo sampling schemes (MC dynamics, MC replica-exchange, and combinations). A particular emphasis is given to the unique design of the CABS force-field, which is largely defined using one-dimensional structural properties of proteins, including protein secondary structure. This chapter also presents CABS-based modeling methods, including multiscale tools for de novo structure prediction, modeling of protein dynamics and prediction of protein-peptide complexes. CABS-based tools are freely available at http://biocomp.chem.uw.edu.pl/tools