Evolutionary algorithm to ab initio protein structure prediction with hydrophobic interactions

Proteins are polymers whose chains are composed of 20 different monomers, called amino acids. The problem of Protein Structure Prediction (PSP) is the determination of protein 3D conformation from its amino acid sequence. Two main strategies are usually employed to work with PSP: homology and Ab initio approaches. This paper presents an Evolutionary Algorithm to PSP using an Ab initio approach (ProtPred). The predictions are evaluated using fitness functions based on potential energies (electrostatic and van der Waals) and hydrophobic interactions. The proposed approach uses dihedral angles and main angles of the lateral chains to model a protein structure. ProtPred is evaluated using relatively complex cases for an Ab initio approach. Results have shown that ProtPred is a consistent approach.

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