All-Atom CSAW:An Ab Initio Protein Folding Method

摘要

Conditioned Self-Avoiding Walk (CSAW) was first developed as a tool to simulate protein folding Based on CSAW algorithm,All-atom Conditioned Self-Avoiding Walk (AA-CSAW) was developed around 2007.The polypeptide chain is simulated as effectively rigid cranks -Ca-CO-NH- units lined by covalent bonds.Bond lengths and bond angles are set as fixed optimal values.All-atom amino acid sidechain is attached to very Ca atom.The structure of polypeptide is fully described by backbone dihedral angles φ,ψ and the sidechain dihedral angles χ.A trial structure is randomly generated by pivoting the polypeptide chain and sidechains.In the pivot algorithm,the backbone dihedral angles φ,ψ for each residue are chosen according to probability distributions in Ramachandran plot.The dihedral angle distributions are improved by 3-residue fragment set investigation.The effective energy of protein structure is constructed by considering hydrophobic effect,desolvation effect and hydrogen bonding interaction.An appropriate three dimensional structure is accepted with a probability according to Metropolis scheme.In order to evaluate the accepted structures in Monte Carlo simulations,the ratio of secondary structure content to radius of gyration is introduced.CASP09 target example shows that AA-CSAW is an efficient and promising ab initio method.