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Flexible Structural Neighborhood—a database of protein structural similarities and alignments
Protein structures are flexible, changing their shapes not only upon substrate binding, but also during evolution as a collective effect of mutations, deletions and insertions. A new generation of protein structure comparison algorithms allows for such flexibility; they go beyond identifying the lar...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347486/ https://www.ncbi.nlm.nih.gov/pubmed/16381864 http://dx.doi.org/10.1093/nar/gkj124 |
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author | Li, Zhanwen Ye, Yuzhen Godzik, Adam |
author_facet | Li, Zhanwen Ye, Yuzhen Godzik, Adam |
author_sort | Li, Zhanwen |
collection | PubMed |
description | Protein structures are flexible, changing their shapes not only upon substrate binding, but also during evolution as a collective effect of mutations, deletions and insertions. A new generation of protein structure comparison algorithms allows for such flexibility; they go beyond identifying the largest common part between two proteins and find hinge regions and patterns of flexibility in protein families. Here we present a Flexible Structural Neighborhood (FSN), a database of structural neighbors of proteins deposited in PDB as seen by a flexible protein structure alignment program FATCAT, developed previously in our group. The database, searchable by a protein PDB code, provides lists of proteins with statistically significant structural similarity and on lower menu levels provides detailed alignments, interactive superposition of structures and positions of hinges that were identified in the comparison. While superficially similar to other structural protein alignment resources, FSN provides a unique resource to study not only protein structural similarity, but also how protein structures change. FSN is available from a server and by direct links from the PDB database. |
format | Text |
id | pubmed-1347486 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-13474862006-01-25 Flexible Structural Neighborhood—a database of protein structural similarities and alignments Li, Zhanwen Ye, Yuzhen Godzik, Adam Nucleic Acids Res Article Protein structures are flexible, changing their shapes not only upon substrate binding, but also during evolution as a collective effect of mutations, deletions and insertions. A new generation of protein structure comparison algorithms allows for such flexibility; they go beyond identifying the largest common part between two proteins and find hinge regions and patterns of flexibility in protein families. Here we present a Flexible Structural Neighborhood (FSN), a database of structural neighbors of proteins deposited in PDB as seen by a flexible protein structure alignment program FATCAT, developed previously in our group. The database, searchable by a protein PDB code, provides lists of proteins with statistically significant structural similarity and on lower menu levels provides detailed alignments, interactive superposition of structures and positions of hinges that were identified in the comparison. While superficially similar to other structural protein alignment resources, FSN provides a unique resource to study not only protein structural similarity, but also how protein structures change. FSN is available from a server and by direct links from the PDB database. Oxford University Press 2006-01-01 2005-12-28 /pmc/articles/PMC1347486/ /pubmed/16381864 http://dx.doi.org/10.1093/nar/gkj124 Text en © The Author 2006. Published by Oxford University Press. All rights reserved |
spellingShingle | Article Li, Zhanwen Ye, Yuzhen Godzik, Adam Flexible Structural Neighborhood—a database of protein structural similarities and alignments |
title | Flexible Structural Neighborhood—a database of protein structural similarities and alignments |
title_full | Flexible Structural Neighborhood—a database of protein structural similarities and alignments |
title_fullStr | Flexible Structural Neighborhood—a database of protein structural similarities and alignments |
title_full_unstemmed | Flexible Structural Neighborhood—a database of protein structural similarities and alignments |
title_short | Flexible Structural Neighborhood—a database of protein structural similarities and alignments |
title_sort | flexible structural neighborhood—a database of protein structural similarities and alignments |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347486/ https://www.ncbi.nlm.nih.gov/pubmed/16381864 http://dx.doi.org/10.1093/nar/gkj124 |
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