An investigation on the use of constraints-applied voxels in the search for protein surface atoms / Ling Wei Lee, and Andrzej Bargiela // W: Proceedings of the World Congress on Engineering 2012, WCE 2012, ... więcej

An investigation on the use of constraints-applied voxels in the search for protein surface atoms / Ling Wei Lee, and Andrzej Bargiela // W: Proceedings of the World Congress on Engineering 2012, WCE 2012, July 4 - 6, 2012, London, U.K. Vol I [Dokument elektroniczny] / eds. : S. I. Ao [et al.]. – [Hong Kong] : Newswood Limited, 2012. – (Lecture Notes in Engineering and Computer Science, ISSN 2078-0966). – [7] s. : rys., schem., tab. – Tryb dostępu: http://www.iaeng.org/publication/WCE2012/WCE2012_pp655-661.pdf. – Bibliogr. 22 poz., Abstr. – ISBN 978-988-19251-3-8

The functionalities of proteins are attributed to atomic arrangements on surfaces which define the reactivity of regions that bind with external agents. A good extraction of protein surface atoms not only ... więcej

The functionalities of proteins are attributed to atomic arrangements on surfaces which define the reactivity of regions that bind with external agents. A good extraction of protein surface atoms not only provides a ready list of dataset for surface studies, but it also reduces the amount of processing required in computer-aided drug design programs by displaying only the exterior portion of the protein. Software methods for molecular surface studies typically implement algorithms of a probe or geometrical nature, with the latter represented as alpha/beta shapes, Voronoi tessellations etc. Grid units and voxels were used in some of the earliest programs for dock sites identification; however the role and contribution of voxels in the extraction of surface atoms has not been investigated. We present here such a method with constraints applied to the voxels in the form of voxel occupancy and atomic membership, and the approach concludes with a ‘peeling’ method for the removal of internal atoms in the extracts. The obtained results are visualised and compared against output from the MSMS and Surface Racer programs for accuracy verification.