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description Publicationkeyboard_double_arrow_right Article 2021 Serbia, Belgium, France, France, Italy, Denmark, Italy, FrancePublisher:Oxford University Press (OUP) Funded by:MESTD | Ministry of Education, Sc..., EC | SMILE, NIH | Gene Ontology Consortium +3 projectsMESTD| Ministry of Education, Science and Technological Development, Republic of Serbia, Grant no. 451-03-68/2020-14/200017 (University of Belgrade, Institute of Nuclear Sciences 'Vinca', Belgrade-Vinca) ,EC| SMILE ,NIH| Gene Ontology Consortium ,EC| IDPfun ,EC| MIMIC ,EC| PhasAGEFederica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor Erdős; Pascale Gaudet; Michelle G. Giglio; Juliana Glavina; Javier Iserte; Valentin Iglesias; Zsofia E. Kalman; Matteo Lambrughi; Emanuela Leonardi; Sonia Longhi; Sandra Macedo-Ribeiro; Emiliano Maiani; Julia Marchetti; Cristina Marino-Buslje; Attila Mészáros; Alexander Miguel Monzon; Giovanni Minervini; Suvarna Nadendla; Juliet F Nilsson; Marian Novotný; Christos A. Ouzounis; Nicolas Palopoli; Elena Papaleo; Pedro Pereira; Gabriele Pozzati; Vasilis J. Promponas; Jordi Pujols; Alma Carolina Sanchez Rocha; Martín N. Salas; Luciana Rodriguez Sawicki; Eva Schad; Aditi Shenoy; Tamás Szaniszló; Konstantinos D. Tsirigos; Nevena Veljkovic; Gustavo Parisi; Salvador Ventura; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto; Damiano Piovesan;The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 100 citations 100 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 71visibility views 71 download downloads 76 Powered bymore_vert Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2021 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | INFERNETEC| INFERNETAuthors: Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco;Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco;AbstractBackgroundBoltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. They are parametrized in terms of local biases accounting for residue conservation, and pairwise terms to model epistatic coevolution between residues. From the model parameters, it is possible to extract an accurate prediction of the three-dimensional contact map of the target domain. More recently, the accuracy of these models has been also assessed in terms of their ability in predicting mutational effects and generatingin silicofunctional sequences.ResultsOur adaptive implementation of Boltzmann machine learning, , can be generally applied to both protein and RNA families and accomplishes several learning set-ups, depending on the complexity of the input data and on the user requirements. The code is fully available athttps://github.com/anna-pa-m/adabmDCA. As an example, we have performed the learning of three Boltzmann machines modeling the Kunitz and Beta-lactamase2 protein domains and TPP-riboswitch RNA domain.ConclusionsThe models learned by are comparable to those obtained by state-of-the-art techniques for this task, in terms of the quality of the inferred contact map as well as of the synthetically generated sequences. In addition, the code implements both equilibrium and out-of-equilibrium learning, which allows for an accurate and lossless training when the equilibrium one is prohibitive in terms of computational time, and allows for pruning irrelevant parameters using an information-based criterion.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8555268Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2021License: CC BYFull-Text: https://hal.science/hal-03410137/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s12859-021-04441-9&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 10 citations 10 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8555268Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2021License: CC BYFull-Text: https://hal.science/hal-03410137/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s12859-021-04441-9&type=result"></script>'); --> </script>
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description Publicationkeyboard_double_arrow_right Article 2021 Serbia, Belgium, France, France, Italy, Denmark, Italy, FrancePublisher:Oxford University Press (OUP) Funded by:MESTD | Ministry of Education, Sc..., EC | SMILE, NIH | Gene Ontology Consortium +3 projectsMESTD| Ministry of Education, Science and Technological Development, Republic of Serbia, Grant no. 451-03-68/2020-14/200017 (University of Belgrade, Institute of Nuclear Sciences 'Vinca', Belgrade-Vinca) ,EC| SMILE ,NIH| Gene Ontology Consortium ,EC| IDPfun ,EC| MIMIC ,EC| PhasAGEFederica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor Erdős; Pascale Gaudet; Michelle G. Giglio; Juliana Glavina; Javier Iserte; Valentin Iglesias; Zsofia E. Kalman; Matteo Lambrughi; Emanuela Leonardi; Sonia Longhi; Sandra Macedo-Ribeiro; Emiliano Maiani; Julia Marchetti; Cristina Marino-Buslje; Attila Mészáros; Alexander Miguel Monzon; Giovanni Minervini; Suvarna Nadendla; Juliet F Nilsson; Marian Novotný; Christos A. Ouzounis; Nicolas Palopoli; Elena Papaleo; Pedro Pereira; Gabriele Pozzati; Vasilis J. Promponas; Jordi Pujols; Alma Carolina Sanchez Rocha; Martín N. Salas; Luciana Rodriguez Sawicki; Eva Schad; Aditi Shenoy; Tamás Szaniszló; Konstantinos D. Tsirigos; Nevena Veljkovic; Gustavo Parisi; Salvador Ventura; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto; Damiano Piovesan;The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 100 citations 100 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 71visibility views 71 download downloads 76 Powered bymore_vert Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2021 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | INFERNETEC| INFERNETAuthors: Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco;Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco;AbstractBackgroundBoltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. They are parametrized in terms of local biases accounting for residue conservation, and pairwise terms to model epistatic coevolution between residues. From the model parameters, it is possible to extract an accurate prediction of the three-dimensional contact map of the target domain. More recently, the accuracy of these models has been also assessed in terms of their ability in predicting mutational effects and generatingin silicofunctional sequences.ResultsOur adaptive implementation of Boltzmann machine learning, , can be generally applied to both protein and RNA families and accomplishes several learning set-ups, depending on the complexity of the input data and on the user requirements. The code is fully available athttps://github.com/anna-pa-m/adabmDCA. As an example, we have performed the learning of three Boltzmann machines modeling the Kunitz and Beta-lactamase2 protein domains and TPP-riboswitch RNA domain.ConclusionsThe models learned by are comparable to those obtained by state-of-the-art techniques for this task, in terms of the quality of the inferred contact map as well as of the synthetically generated sequences. In addition, the code implements both equilibrium and out-of-equilibrium learning, which allows for an accurate and lossless training when the equilibrium one is prohibitive in terms of computational time, and allows for pruning irrelevant parameters using an information-based criterion.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8555268Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2021License: CC BYFull-Text: https://hal.science/hal-03410137/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s12859-021-04441-9&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 10 citations 10 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8555268Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2021License: CC BYFull-Text: https://hal.science/hal-03410137/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s12859-021-04441-9&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu