Cargando…

Structural footprinting in protein structure comparison: the impact of structural fragments

BACKGROUND: One approach for speeding-up protein structure comparison is the projection approach, where a protein structure is mapped to a high-dimensional vector and structural similarity is approximated by distance between the corresponding vectors. Structural footprinting methods are projection m...

Descripción completa

Detalles Bibliográficos
Autores principales: Zotenko, Elena, Islamaj Dogan, Rezarta, Wilbur, W John, O'Leary, Dianne P, Przytycka, Teresa M
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2082327/
https://www.ncbi.nlm.nih.gov/pubmed/17688700
http://dx.doi.org/10.1186/1472-6807-7-53
_version_ 1782138171369193472
author Zotenko, Elena
Islamaj Dogan, Rezarta
Wilbur, W John
O'Leary, Dianne P
Przytycka, Teresa M
author_facet Zotenko, Elena
Islamaj Dogan, Rezarta
Wilbur, W John
O'Leary, Dianne P
Przytycka, Teresa M
author_sort Zotenko, Elena
collection PubMed
description BACKGROUND: One approach for speeding-up protein structure comparison is the projection approach, where a protein structure is mapped to a high-dimensional vector and structural similarity is approximated by distance between the corresponding vectors. Structural footprinting methods are projection methods that employ the same general technique to produce the mapping: first select a representative set of structural fragments as models and then map a protein structure to a vector in which each dimension corresponds to a particular model and "counts" the number of times the model appears in the structure. The main difference between any two structural footprinting methods is in the set of models they use; in fact a large number of methods can be generated by varying the type of structural fragments used and the amount of detail in their representation. How do these choices affect the ability of the method to detect various types of structural similarity? RESULTS: To answer this question we benchmarked three structural footprinting methods that vary significantly in their selection of models against the CATH database. In the first set of experiments we compared the methods' ability to detect structural similarity characteristic of evolutionarily related structures, i.e., structures within the same CATH superfamily. In the second set of experiments we tested the methods' agreement with the boundaries imposed by classification groups at the Class, Architecture, and Fold levels of the CATH hierarchy. CONCLUSION: In both experiments we found that the method which uses secondary structure information has the best performance on average, but no one method performs consistently the best across all groups at a given classification level. We also found that combining the methods' outputs significantly improves the performance. Moreover, our new techniques to measure and visualize the methods' agreement with the CATH hierarchy, including the threshholded affinity graph, are useful beyond this work. In particular, they can be used to expose a similar composition of different classification groups in terms of structural fragments used by the method and thus provide an alternative demonstration of the continuous nature of the protein structure universe.
format Text
id pubmed-2082327
institution National Center for Biotechnology Information
language English
publishDate 2007
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-20823272007-11-21 Structural footprinting in protein structure comparison: the impact of structural fragments Zotenko, Elena Islamaj Dogan, Rezarta Wilbur, W John O'Leary, Dianne P Przytycka, Teresa M BMC Struct Biol Research Article BACKGROUND: One approach for speeding-up protein structure comparison is the projection approach, where a protein structure is mapped to a high-dimensional vector and structural similarity is approximated by distance between the corresponding vectors. Structural footprinting methods are projection methods that employ the same general technique to produce the mapping: first select a representative set of structural fragments as models and then map a protein structure to a vector in which each dimension corresponds to a particular model and "counts" the number of times the model appears in the structure. The main difference between any two structural footprinting methods is in the set of models they use; in fact a large number of methods can be generated by varying the type of structural fragments used and the amount of detail in their representation. How do these choices affect the ability of the method to detect various types of structural similarity? RESULTS: To answer this question we benchmarked three structural footprinting methods that vary significantly in their selection of models against the CATH database. In the first set of experiments we compared the methods' ability to detect structural similarity characteristic of evolutionarily related structures, i.e., structures within the same CATH superfamily. In the second set of experiments we tested the methods' agreement with the boundaries imposed by classification groups at the Class, Architecture, and Fold levels of the CATH hierarchy. CONCLUSION: In both experiments we found that the method which uses secondary structure information has the best performance on average, but no one method performs consistently the best across all groups at a given classification level. We also found that combining the methods' outputs significantly improves the performance. Moreover, our new techniques to measure and visualize the methods' agreement with the CATH hierarchy, including the threshholded affinity graph, are useful beyond this work. In particular, they can be used to expose a similar composition of different classification groups in terms of structural fragments used by the method and thus provide an alternative demonstration of the continuous nature of the protein structure universe. BioMed Central 2007-08-09 /pmc/articles/PMC2082327/ /pubmed/17688700 http://dx.doi.org/10.1186/1472-6807-7-53 Text en Copyright © 2007 Zotenko 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 Research Article
Zotenko, Elena
Islamaj Dogan, Rezarta
Wilbur, W John
O'Leary, Dianne P
Przytycka, Teresa M
Structural footprinting in protein structure comparison: the impact of structural fragments
title Structural footprinting in protein structure comparison: the impact of structural fragments
title_full Structural footprinting in protein structure comparison: the impact of structural fragments
title_fullStr Structural footprinting in protein structure comparison: the impact of structural fragments
title_full_unstemmed Structural footprinting in protein structure comparison: the impact of structural fragments
title_short Structural footprinting in protein structure comparison: the impact of structural fragments
title_sort structural footprinting in protein structure comparison: the impact of structural fragments
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2082327/
https://www.ncbi.nlm.nih.gov/pubmed/17688700
http://dx.doi.org/10.1186/1472-6807-7-53
work_keys_str_mv AT zotenkoelena structuralfootprintinginproteinstructurecomparisontheimpactofstructuralfragments
AT islamajdoganrezarta structuralfootprintinginproteinstructurecomparisontheimpactofstructuralfragments
AT wilburwjohn structuralfootprintinginproteinstructurecomparisontheimpactofstructuralfragments
AT olearydiannep structuralfootprintinginproteinstructurecomparisontheimpactofstructuralfragments
AT przytyckateresam structuralfootprintinginproteinstructurecomparisontheimpactofstructuralfragments