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MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature

Shivashankar, Nithin and Patil, Sonali and Bhosle, Amrisha and Chandra, Nagasuma and Natarajan, Vijay (2016) MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. In: BMC BIOINFORMATICS, 17 .

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Official URL: http://dx.doi.org/10.1186/s12859-015-0874-8

Abstract

Background: Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data. Methods: We present a Multi-Scale Morse-Smale Molecular-Surface Alignment tool, MS3ALIGN, which aligns molecular surfaces based on significant protrusions on the molecular surface. The input is a pair of molecular surfaces represented as triangle meshes. A key advantage of MS3ALIGN is computational efficiency that is achieved because it processes only a few carefully chosen protrusions on the molecular surface. Furthermore, the alignments are partial in nature and therefore allows for inexact surfaces to be aligned. Results: The method is evaluated in four settings. First, we establish performance using known alignments with varying overlap and noise values. Second, we compare the method with SurfComp, an existing surface alignment method. We show that we are able to determine alignments reported by SurfComp, as well as report relevant alignments not found by SurfComp. Third, we validate the ability of MS3ALIGN to determine alignments in the case of structurally dissimilar binding sites. Fourth, we demonstrate the ability of MS3ALIGN to align iso-surfaces derived from cryo-electron microscopy scans. Conclusions: We have presented an algorithm that aligns Molecular Surfaces based on the topology of surface curvature. Awebserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet. in/ms3align.

Item Type: Journal Article
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Additional Information: Copy right for this article belongs to the BIOMED CENTRAL LTD, 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND
Keywords: Molecular alignments; Molecular surfaces
Department/Centre: Division of Biological Sciences > Biochemistry
Division of Electrical Sciences > Computer Science & Automation (Formerly, School of Automation)
Division of Information Sciences > Supercomputer Education & Research Centre
Date Deposited: 18 Feb 2016 06:12
Last Modified: 18 Feb 2016 06:12
URI: http://eprints.iisc.ernet.in/id/eprint/53274

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