Finding protein-protein interaction patterns by contact map matching.
Autor(a) principal: | |
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Data de Publicação: | 2007 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/969 |
Resumo: | We propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can compare protein-protein interaction maps and also obtain a dissimilarity score between them. The same algorithm used to compare the maps can align the contacts of all the complexes and be helpful in the determination of a pattern of conserved interactions at the interfaces. We present an example for the application of this method by analyzing the pattern of interaction of bovine pancreatic trypsin inhibitors and trypsins, chymotrypsins, a thrombin, a matriptase, and a kallikrein - all classified as serine proteases. We found 20 contacts conserved in trypsins and chymotrypsins and 3 specific ones are present in all the serine protease complexes studied. The method was able to identify important contacts for the protein family studied and the results are in agreement with the literature. |
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Finding protein-protein interaction patterns by contact map matching.BioinformáticaInteração proteína-proteínaMapas de contatoContact mapsSerine proteasesBioinformaticsSerine proteinasesprotein-protein interactionsWe propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can compare protein-protein interaction maps and also obtain a dissimilarity score between them. The same algorithm used to compare the maps can align the contacts of all the complexes and be helpful in the determination of a pattern of conserved interactions at the interfaces. We present an example for the application of this method by analyzing the pattern of interaction of bovine pancreatic trypsin inhibitors and trypsins, chymotrypsins, a thrombin, a matriptase, and a kallikrein - all classified as serine proteases. We found 20 contacts conserved in trypsins and chymotrypsins and 3 specific ones are present in all the serine protease complexes studied. The method was able to identify important contacts for the protein family studied and the results are in agreement with the literature.UFMG; UFMG; UFMG; UFMG; UFMG; GORAN NESHICH, CNPTIA; UFMG; UFMG; UFMG.MELO, R. C.RIBEIRO, C.MURRAY, C. S.VELOSO, C. J. M.SILVEIRA, C. H. daNESHICH, G.MEIRA JUNIOR, W.CARCERONI, R. L.SANTORO, M. M.2011-04-10T11:11:11Z2011-04-10T11:11:11Z2007-12-0720072017-05-11T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleGenetics and Molecular Research, v. 6, n. 4, p. 946-963, 2007.http://www.alice.cnptia.embrapa.br/alice/handle/doc/969enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2017-05-12T01:37:52Zoai:www.alice.cnptia.embrapa.br:doc/969Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542017-05-12T01:37:52falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542017-05-12T01:37:52Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
Finding protein-protein interaction patterns by contact map matching. |
title |
Finding protein-protein interaction patterns by contact map matching. |
spellingShingle |
Finding protein-protein interaction patterns by contact map matching. MELO, R. C. Bioinformática Interação proteína-proteína Mapas de contato Contact maps Serine proteases Bioinformatics Serine proteinases protein-protein interactions |
title_short |
Finding protein-protein interaction patterns by contact map matching. |
title_full |
Finding protein-protein interaction patterns by contact map matching. |
title_fullStr |
Finding protein-protein interaction patterns by contact map matching. |
title_full_unstemmed |
Finding protein-protein interaction patterns by contact map matching. |
title_sort |
Finding protein-protein interaction patterns by contact map matching. |
author |
MELO, R. C. |
author_facet |
MELO, R. C. RIBEIRO, C. MURRAY, C. S. VELOSO, C. J. M. SILVEIRA, C. H. da NESHICH, G. MEIRA JUNIOR, W. CARCERONI, R. L. SANTORO, M. M. |
author_role |
author |
author2 |
RIBEIRO, C. MURRAY, C. S. VELOSO, C. J. M. SILVEIRA, C. H. da NESHICH, G. MEIRA JUNIOR, W. CARCERONI, R. L. SANTORO, M. M. |
author2_role |
author author author author author author author author |
dc.contributor.none.fl_str_mv |
UFMG; UFMG; UFMG; UFMG; UFMG; GORAN NESHICH, CNPTIA; UFMG; UFMG; UFMG. |
dc.contributor.author.fl_str_mv |
MELO, R. C. RIBEIRO, C. MURRAY, C. S. VELOSO, C. J. M. SILVEIRA, C. H. da NESHICH, G. MEIRA JUNIOR, W. CARCERONI, R. L. SANTORO, M. M. |
dc.subject.por.fl_str_mv |
Bioinformática Interação proteína-proteína Mapas de contato Contact maps Serine proteases Bioinformatics Serine proteinases protein-protein interactions |
topic |
Bioinformática Interação proteína-proteína Mapas de contato Contact maps Serine proteases Bioinformatics Serine proteinases protein-protein interactions |
description |
We propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can compare protein-protein interaction maps and also obtain a dissimilarity score between them. The same algorithm used to compare the maps can align the contacts of all the complexes and be helpful in the determination of a pattern of conserved interactions at the interfaces. We present an example for the application of this method by analyzing the pattern of interaction of bovine pancreatic trypsin inhibitors and trypsins, chymotrypsins, a thrombin, a matriptase, and a kallikrein - all classified as serine proteases. We found 20 contacts conserved in trypsins and chymotrypsins and 3 specific ones are present in all the serine protease complexes studied. The method was able to identify important contacts for the protein family studied and the results are in agreement with the literature. |
publishDate |
2007 |
dc.date.none.fl_str_mv |
2007-12-07 2007 2011-04-10T11:11:11Z 2011-04-10T11:11:11Z 2017-05-11T11:11:11Z |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Genetics and Molecular Research, v. 6, n. 4, p. 946-963, 2007. http://www.alice.cnptia.embrapa.br/alice/handle/doc/969 |
identifier_str_mv |
Genetics and Molecular Research, v. 6, n. 4, p. 946-963, 2007. |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/969 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
_version_ |
1794503435998986240 |