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Layers: A molecular surface peeling algorithm and its applications to analyze protein structures

We present an algorithm ‘Layers’ to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and h...

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Autores principales: Karampudi, Naga Bhushana Rao, Bahadur, Ranjit Prasad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4639851/
https://www.ncbi.nlm.nih.gov/pubmed/26553411
http://dx.doi.org/10.1038/srep16141
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author Karampudi, Naga Bhushana Rao
Bahadur, Ranjit Prasad
author_facet Karampudi, Naga Bhushana Rao
Bahadur, Ranjit Prasad
author_sort Karampudi, Naga Bhushana Rao
collection PubMed
description We present an algorithm ‘Layers’ to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest classifier to predict the RTP of a given polypeptide sequence. Layers is a standalone application; however, it can be merged with other applications to reduce the computational load when working with large datasets of protein structures. Layers is available freely at http://www.csb.iitkgp.ernet.in/applications/mol_layers/main.
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spelling pubmed-46398512015-11-16 Layers: A molecular surface peeling algorithm and its applications to analyze protein structures Karampudi, Naga Bhushana Rao Bahadur, Ranjit Prasad Sci Rep Article We present an algorithm ‘Layers’ to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest classifier to predict the RTP of a given polypeptide sequence. Layers is a standalone application; however, it can be merged with other applications to reduce the computational load when working with large datasets of protein structures. Layers is available freely at http://www.csb.iitkgp.ernet.in/applications/mol_layers/main. Nature Publishing Group 2015-11-10 /pmc/articles/PMC4639851/ /pubmed/26553411 http://dx.doi.org/10.1038/srep16141 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Karampudi, Naga Bhushana Rao
Bahadur, Ranjit Prasad
Layers: A molecular surface peeling algorithm and its applications to analyze protein structures
title Layers: A molecular surface peeling algorithm and its applications to analyze protein structures
title_full Layers: A molecular surface peeling algorithm and its applications to analyze protein structures
title_fullStr Layers: A molecular surface peeling algorithm and its applications to analyze protein structures
title_full_unstemmed Layers: A molecular surface peeling algorithm and its applications to analyze protein structures
title_short Layers: A molecular surface peeling algorithm and its applications to analyze protein structures
title_sort layers: a molecular surface peeling algorithm and its applications to analyze protein structures
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4639851/
https://www.ncbi.nlm.nih.gov/pubmed/26553411
http://dx.doi.org/10.1038/srep16141
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