Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential

Computational Biology and Chemistry
Takuyo AitaYuzuru Husimi

Abstract

In vitro molecular evolution creates a lot of peptide aptamers that bind to each target protein. In many cases, their binding sites on a protein surface are not known. Then, predicting the binding sites through computation within a reasonable time is desirable. With this aim, we have developed a novel system of fast and robust blind docking of a peptide to a fixed protein structure at low computational costs. Our algorithm is based on the following scheme. Representing each of the amino acid residues by a single point corresponding to its side-chain center, the structure of a target protein and that of a ligand peptide are coarse-grained. The peptide, which is described as a flexible bead model, is movable along the grid-points which are set surrounding the protein. An arbitrary state of the protein-peptide complex is subjected to Delaunay tessellation. Then, the fitness of a peptide-coordination to the protein is measured by a four-body statistical pseudo-potential. Through 1000 trials of a simple hill-climbing optimization, the best 15 peptide-coordinations with the 1st-15th highest fitness values are selected as candidates for the putative coordination. Retrieving the available 28 protein-peptide complexes from the Protein D...Continue Reading

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Citations

Aug 25, 2012·Future Medicinal Chemistry·Joseph Audie, Jon Swanson
Apr 23, 2015·Briefings in Bioinformatics·Robert Rentzsch, Bernhard Y Renard
May 7, 2016·European Journal of Medicinal Chemistry·Margherita BrindisiSandra Gemma
Dec 14, 2011·Structure·Onur DagliyanNikolay V Dokholyan

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