Publications of Giampaolo Liuzzi

This page shows all publications that appeared in the IASI annual research reports. Authors currently affiliated with the Institute are always listed with the full name.

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IASI Research Report n. 12-25  (Previous    Next)  

Lampariello F., Giampaolo Liuzzi

Global optimization of protein-peptide docking by a filling function method

ABSTRACT
Molecular docking programs play a crucial role in drug design and development. In recent years, much attention has been devoted to the protein-peptide docking problem in which docking of a flexible peptide with a given protein is sought. In this work we present a docking algorithm which is based on the use of a filling function method for continuous global optimization. In particular, the protein-peptide docking position is found by minimizing the conformational potential energy function based on an appropriate mathematical model. The resulting global optimization problem presents some difficulties, since it is a large-scale one and the objective function is non-convex, so that it has many local minima. The method consists in modifying the potential function by adding to it a term in order to fill the basin of a local minimum. This allows to escape from that local solution and moreover, by properly exploiting the filling strategy, to explore large regions in the peptide positional and conformational space. Moreover, in order to obtain more accurate results, we search the solution by performing a two-phase optimization process. In particular, in a first step only the carbon $C_alpha$ atoms of the protein and peptide are considered thus obtaining an approximate docking solution. Then, the energy function is completed by considering all the peptide and protein atoms so that starting from the solution of the first phase, the new minimization process gives a more accurate result. We present numerical results on a set of benchmark docking pairs and their comparison with those obtained by the well-known software package PacthDock for molecular docking.
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