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

摘要

Despite the significant increase in computational power, molecular modelingof 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 ismultiscale modeling to merge all-atom and coarse-grained models. This chapterdescribes a well-established CABS coarse-grained protein model. The CABS(C-Alpha, C-Beta and Side chains) model assumes a 2-4 united-atomrepresentation of amino acids, knowledge-based force field (derived from thestatistical regularities seen in known protein sequences and structures) andefficient Monte Carlo sampling schemes (MC dynamics, MC replica-exchange, andcombinations). A particular emphasis is given to the unique design of the CABSforce-field, which is largely defined using one-dimensional structuralproperties of proteins, including protein secondary structure. This chapteralso presents CABS-based modeling methods, including multiscale tools for denovo structure prediction, modeling of protein dynamics and prediction ofprotein-peptide complexes. CABS-based tools are freely available athttp://biocomp.chem.uw.edu.pl/tools