SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10316/101280 https://doi.org/10.3390/ijms21197281 |
Resumo: | Protein Hot-Spots (HS) are experimentally determined amino acids, key to small ligand binding and tend to be structural landmarks on protein-protein interactions. As such, they were extensively approached by structure-based Machine Learning (ML) prediction methods. However, the availability of a much larger array of protein sequences in comparison to determined tree-dimensional structures indicates that a sequence-based HS predictor has the potential to be more useful for the scientific community. Herein, we present SPOTONE, a new ML predictor able to accurately classify protein HS via sequence-only features. This algorithm shows accuracy, AUROC, precision, recall and F1-score of 0.82, 0.83, 0.91, 0.82 and 0.85, respectively, on an independent testing set. The algorithm is deployed within a free-to-use webserver at http://moreiralab.com/resources/spotone, only requiring the user to submit a FASTA file with one or more protein sequences. |
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SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Featuresbig-data; hot-spots; machine learning; protein–protein complexes; structural biologyAmino Acid SequenceAmino AcidsBinding SitesComputational BiologyDatabases, ProteinDatasets as TopicHumansProtein BindingProtein Interaction MappingProteinsMachine LearningProtein Hot-Spots (HS) are experimentally determined amino acids, key to small ligand binding and tend to be structural landmarks on protein-protein interactions. As such, they were extensively approached by structure-based Machine Learning (ML) prediction methods. However, the availability of a much larger array of protein sequences in comparison to determined tree-dimensional structures indicates that a sequence-based HS predictor has the potential to be more useful for the scientific community. Herein, we present SPOTONE, a new ML predictor able to accurately classify protein HS via sequence-only features. This algorithm shows accuracy, AUROC, precision, recall and F1-score of 0.82, 0.83, 0.91, 0.82 and 0.85, respectively, on an independent testing set. The algorithm is deployed within a free-to-use webserver at http://moreiralab.com/resources/spotone, only requiring the user to submit a FASTA file with one or more protein sequences.2020-10-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://hdl.handle.net/10316/101280http://hdl.handle.net/10316/101280https://doi.org/10.3390/ijms21197281eng1422-0067Preto, A. J.Moreira, Irina S.info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2022-08-19T20:39:38Zoai:estudogeral.uc.pt:10316/101280Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T21:18:30.537406Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features |
title |
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features |
spellingShingle |
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features Preto, A. J. big-data; hot-spots; machine learning; protein–protein complexes; structural biology Amino Acid Sequence Amino Acids Binding Sites Computational Biology Databases, Protein Datasets as Topic Humans Protein Binding Protein Interaction Mapping Proteins Machine Learning |
title_short |
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features |
title_full |
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features |
title_fullStr |
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features |
title_full_unstemmed |
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features |
title_sort |
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features |
author |
Preto, A. J. |
author_facet |
Preto, A. J. Moreira, Irina S. |
author_role |
author |
author2 |
Moreira, Irina S. |
author2_role |
author |
dc.contributor.author.fl_str_mv |
Preto, A. J. Moreira, Irina S. |
dc.subject.por.fl_str_mv |
big-data; hot-spots; machine learning; protein–protein complexes; structural biology Amino Acid Sequence Amino Acids Binding Sites Computational Biology Databases, Protein Datasets as Topic Humans Protein Binding Protein Interaction Mapping Proteins Machine Learning |
topic |
big-data; hot-spots; machine learning; protein–protein complexes; structural biology Amino Acid Sequence Amino Acids Binding Sites Computational Biology Databases, Protein Datasets as Topic Humans Protein Binding Protein Interaction Mapping Proteins Machine Learning |
description |
Protein Hot-Spots (HS) are experimentally determined amino acids, key to small ligand binding and tend to be structural landmarks on protein-protein interactions. As such, they were extensively approached by structure-based Machine Learning (ML) prediction methods. However, the availability of a much larger array of protein sequences in comparison to determined tree-dimensional structures indicates that a sequence-based HS predictor has the potential to be more useful for the scientific community. Herein, we present SPOTONE, a new ML predictor able to accurately classify protein HS via sequence-only features. This algorithm shows accuracy, AUROC, precision, recall and F1-score of 0.82, 0.83, 0.91, 0.82 and 0.85, respectively, on an independent testing set. The algorithm is deployed within a free-to-use webserver at http://moreiralab.com/resources/spotone, only requiring the user to submit a FASTA file with one or more protein sequences. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-10-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10316/101280 http://hdl.handle.net/10316/101280 https://doi.org/10.3390/ijms21197281 |
url |
http://hdl.handle.net/10316/101280 https://doi.org/10.3390/ijms21197281 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
1422-0067 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799134079714590720 |