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

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...

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Autores principales: Shivashankar, Nithin, Patil, Sonali, Bhosle, Amrisha, Chandra, Nagasuma, Natarajan, Vijay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4710026/
https://www.ncbi.nlm.nih.gov/pubmed/26753741
http://dx.doi.org/10.1186/s12859-015-0874-8
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author Shivashankar, Nithin
Patil, Sonali
Bhosle, Amrisha
Chandra, Nagasuma
Natarajan, Vijay
author_facet Shivashankar, Nithin
Patil, Sonali
Bhosle, Amrisha
Chandra, Nagasuma
Natarajan, Vijay
author_sort Shivashankar, Nithin
collection PubMed
description 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. A webserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet.in/ms3align. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0874-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-47100262016-01-13 MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature Shivashankar, Nithin Patil, Sonali Bhosle, Amrisha Chandra, Nagasuma Natarajan, Vijay BMC Bioinformatics Research Article 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. A webserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet.in/ms3align. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0874-8) contains supplementary material, which is available to authorized users. BioMed Central 2016-01-12 /pmc/articles/PMC4710026/ /pubmed/26753741 http://dx.doi.org/10.1186/s12859-015-0874-8 Text en © Shivashankar et al. 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Shivashankar, Nithin
Patil, Sonali
Bhosle, Amrisha
Chandra, Nagasuma
Natarajan, Vijay
MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature
title MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature
title_full MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature
title_fullStr MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature
title_full_unstemmed MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature
title_short MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature
title_sort ms3align: an efficient molecular surface aligner using the topology of surface curvature
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4710026/
https://www.ncbi.nlm.nih.gov/pubmed/26753741
http://dx.doi.org/10.1186/s12859-015-0874-8
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