engleski

Correlating protein surface shape and hydrophobicity using spherical harmonical expansions

Ability to efficiently match different surface properties is essential for the search phase of a docking procedure. Following the earlier work [1, 2] we implemented a docking search algorithm that uses expansions of surface properties - shape and hydrophobicity - into series of spherical harmonics and special radial functions. Correlation between two surfaces is thereafter performed using the expansion coefficients. For the docking search it is necessary to transform 3 rotational and 3 translational degrees of freedom into 5 rotational and 1 translational. Rotations are performed by applying the Wigner rotational matrices to the expansion coefficients. This method is computationally less expensive than the concurrent Cartesian correlation scheme. Hydrophobicity is mapped onto the protein surface by assigning to the surface regions values 1 and zero, for those belonging to hydrophobic amino acids residues and otherwise, respectively. Obtained results suggest that the method is feasible and that correlating hydrophobicity may be helpful in better ranking docked complexes, albeit more testing is needed.

Protein ; Docking ; Spherical Harmonics ; Hydrophobicity ; Shape Correlation

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