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Fragnostic: walking through protein structure space
The Fragnostic () web tool implements a novel and useful view of protein structure space. We mined a non-redundant subset of the PDB for common fragments shared between proteins inhabiting different SCOP folds. Subsequently, we formulated an inter-fold similarity measure based on fragment sharing. F...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2005
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160124/ https://www.ncbi.nlm.nih.gov/pubmed/15980462 http://dx.doi.org/10.1093/nar/gki363 |
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author | Friedberg, Iddo Godzik, Adam |
author_facet | Friedberg, Iddo Godzik, Adam |
author_sort | Friedberg, Iddo |
collection | PubMed |
description | The Fragnostic () web tool implements a novel and useful view of protein structure space. We mined a non-redundant subset of the PDB for common fragments shared between proteins inhabiting different SCOP folds. Subsequently, we formulated an inter-fold similarity measure based on fragment sharing. Fold space is described as a graph whose nodes are folds between which the edges are drawn depending on the extent of fragment sharing. In this fashion, Fragnostic helps discover meaningful relationships between proteins belonging to different folds, based on sharing similar fragments in the proteins comprising those folds. Distant fold similarity information is supplemented by annotations taken from Gene Ontology, SCOP and CATH. Overall, Fragnostic is a tool which helps discover structural and functional relationships between proteins which are distantly related or seemingly unrelated. |
format | Text |
id | pubmed-1160124 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-11601242005-06-29 Fragnostic: walking through protein structure space Friedberg, Iddo Godzik, Adam Nucleic Acids Res Article The Fragnostic () web tool implements a novel and useful view of protein structure space. We mined a non-redundant subset of the PDB for common fragments shared between proteins inhabiting different SCOP folds. Subsequently, we formulated an inter-fold similarity measure based on fragment sharing. Fold space is described as a graph whose nodes are folds between which the edges are drawn depending on the extent of fragment sharing. In this fashion, Fragnostic helps discover meaningful relationships between proteins belonging to different folds, based on sharing similar fragments in the proteins comprising those folds. Distant fold similarity information is supplemented by annotations taken from Gene Ontology, SCOP and CATH. Overall, Fragnostic is a tool which helps discover structural and functional relationships between proteins which are distantly related or seemingly unrelated. Oxford University Press 2005-07-01 2005-06-27 /pmc/articles/PMC1160124/ /pubmed/15980462 http://dx.doi.org/10.1093/nar/gki363 Text en © The Author 2005. Published by Oxford University Press. All rights reserved |
spellingShingle | Article Friedberg, Iddo Godzik, Adam Fragnostic: walking through protein structure space |
title | Fragnostic: walking through protein structure space |
title_full | Fragnostic: walking through protein structure space |
title_fullStr | Fragnostic: walking through protein structure space |
title_full_unstemmed | Fragnostic: walking through protein structure space |
title_short | Fragnostic: walking through protein structure space |
title_sort | fragnostic: walking through protein structure space |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160124/ https://www.ncbi.nlm.nih.gov/pubmed/15980462 http://dx.doi.org/10.1093/nar/gki363 |
work_keys_str_mv | AT friedbergiddo fragnosticwalkingthroughproteinstructurespace AT godzikadam fragnosticwalkingthroughproteinstructurespace |