Testing Direct Coupling Analysis on HP Model Proteins

University essay from Lunds universitet/Beräkningsbiologi och biologisk fysik; Lunds universitet/Institutionen för astronomi och teoretisk fysik

Abstract: Direct coupling analysis (DCA) models correlations in sets of related (homologous) protein sequences using a Potts-like spin model ansatz. From the couplings of the Potts model, derived by inverse statistical mechanics, residue-pair contacts in the 3D structure of the protein are predicted. In this thesis, this approach is applied to structures from the HP model on a square lattice. All HP sequences folding to the structures studied are known from previous work. For the calculation of the couplings, a maximum likelihood procedure is implemented, based on gradient descent and Monte Carlo methods.

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