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GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures
BACKGROUND: It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs) or"foldons" play a key role in protein folding. A knowl...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275735/ https://www.ncbi.nlm.nih.gov/pubmed/18325123 http://dx.doi.org/10.1186/1472-6807-8-15 |
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author | Laborde, Thomas Tomita, Masaru Krishnan, Arun |
author_facet | Laborde, Thomas Tomita, Masaru Krishnan, Arun |
author_sort | Laborde, Thomas |
collection | PubMed |
description | BACKGROUND: It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs) or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process. Such AFUs can also be used as model systems in order to study the structural organization of proteins. RESULTS: In an earlier work, we had utilized a global network partitioning algorithm to identify modules in proteins. We had shown that these modules correlate well with AFUs. In this work, we have developed a webserver, GANDivAWeb, to identify early folding units or "foldons" in networks using the algorithm described earlier. The website has three functionalities: (a) It is able to display information on the modularity of a database of 1420 proteins used in the original work, (b) It can take as input an uploaded PDB file, identify the modules using the GANDivA algorithm and email the results back to the user and (c) It can take as input an uploaded PDB file and a results file (obtained from functionality (b)) and display the results using the embedded viewer. The results include the module decomposition of the protein, plots of cartoon representations of the protein colored by module identity and connectivity as well as contour plots of the hydrophobicity and relative accessible surface area (RASA) distributions. CONCLUSION: We believe that the GANDivAWeb server, will be a useful tool for scientists interested in the phenomena of protein folding as well as in protein engineering. Our tool not only provides a knowledge of the AFUs through a natural graph partitioning approach but is also able to identify residues that are critical during folding. It is our intention to use this tool to study the topological determinants of protein folding by analyzing the topological changes in proteins over the unfolding/folding pathways. |
format | Text |
id | pubmed-2275735 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-22757352008-03-28 GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures Laborde, Thomas Tomita, Masaru Krishnan, Arun BMC Struct Biol Software BACKGROUND: It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs) or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process. Such AFUs can also be used as model systems in order to study the structural organization of proteins. RESULTS: In an earlier work, we had utilized a global network partitioning algorithm to identify modules in proteins. We had shown that these modules correlate well with AFUs. In this work, we have developed a webserver, GANDivAWeb, to identify early folding units or "foldons" in networks using the algorithm described earlier. The website has three functionalities: (a) It is able to display information on the modularity of a database of 1420 proteins used in the original work, (b) It can take as input an uploaded PDB file, identify the modules using the GANDivA algorithm and email the results back to the user and (c) It can take as input an uploaded PDB file and a results file (obtained from functionality (b)) and display the results using the embedded viewer. The results include the module decomposition of the protein, plots of cartoon representations of the protein colored by module identity and connectivity as well as contour plots of the hydrophobicity and relative accessible surface area (RASA) distributions. CONCLUSION: We believe that the GANDivAWeb server, will be a useful tool for scientists interested in the phenomena of protein folding as well as in protein engineering. Our tool not only provides a knowledge of the AFUs through a natural graph partitioning approach but is also able to identify residues that are critical during folding. It is our intention to use this tool to study the topological determinants of protein folding by analyzing the topological changes in proteins over the unfolding/folding pathways. BioMed Central 2008-03-07 /pmc/articles/PMC2275735/ /pubmed/18325123 http://dx.doi.org/10.1186/1472-6807-8-15 Text en Copyright © 2008 Laborde et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Laborde, Thomas Tomita, Masaru Krishnan, Arun GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures |
title | GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures |
title_full | GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures |
title_fullStr | GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures |
title_full_unstemmed | GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures |
title_short | GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures |
title_sort | gandivaweb: a web server for detecting early folding units ("foldons") from protein 3d structures |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275735/ https://www.ncbi.nlm.nih.gov/pubmed/18325123 http://dx.doi.org/10.1186/1472-6807-8-15 |
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