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PPIDomainMiner: Inferring domain-domain interactions from multiple sources of proteinprotein interactions

Autor: Devignes Marie-Dominique, Najjar Hiba, Alborzi Seyed Ziaeddine, David W. Ritchie, Ahmed-Nacer Amina

Publikováno v: PLoS Computational Biology
PLoS Computational Biology, 2021, 17 (8), pp.e1008844. ⟨10.1371/journal.pcbi.1008844⟩
PLoS Computational Biology, Public Library of Science, 2021, 17 (8), pp.e1008844. ⟨10.1371/journal.pcbi.1008844⟩
PLoS Computational Biology, Vol 17, Iss 8, p e1008844 (2021)

Many biological processes are mediated by protein-protein interactions (PPIs). Because protein domains are the building blocks of proteins, PPIs likely rely on domain-domain interactions (DDIs). Several attempts exist to infer DDIs from PPI networks

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::268da0997ef49fb80c809c93dbb6ceb6
https://hal.science/hal-03435140

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Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus

Autor: Carlos A. García-Pérez, Edgar E. Lara-Ramírez, Juan García Navarro, Xianwu Guo, Diego Alonso Gómez Aguilar

Publikováno v: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-9 (2018)
BMC Bioinformatics

Background The influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen. Results In this study, a data mining approach was employed to extract influ

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b3599a16ff7442cba93352b0e44846f9
https://doi.org/10.1186/s12859-018-2237-8

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3did: a catalog of domain-based interactions of known three-dimensional structure

Autor: Arnaud Ceol, Amelie Stein, Roger Olivella, Roberto Mosca, Patrick Aloy

Publikováno v: Nucleic Acids Research

The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifie

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::64e7cbf60d56e576504fd9b32a2a9a8b
https://doi.org/10.1093/nar/gkt887

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DIMA 3.0: Domain Interaction Map

Autor: Philipp Pagel, Dmitrij Frishman, Baiba Vilne, Qibin Luo

Publikováno v: Nucleic Acids Res. 39, 1, D724-D729 (2011)
Nucleic Acids Research

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3340a95c187f7d87d34639a9d6c1f575
https://doi.org/10.1093/nar/gkq1200

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3did: identification and classification of domain-based interactions of known three-dimensional structure

Autor: Arnaud Ceol, Patrick Aloy, Amelie Stein

Publikováno v: Nucleic Acids Research; Vol 39
Nucleic Acids Research

The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. 3did exploits the availability of structural data to provide molecular details on i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f8170cbe27f071fb125d35606b6e9e77
https://doi.org/10.1093/nar/gkq962

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DIMA 2.0—predicted and known domain interactions

Autor: Normann Strack, Oksana Tovstukhina, Volker Stümpflen, Matthias Oesterheld, Dmitrij Frishman, Philipp Pagel

Publikováno v: Nucleic Acids Research
Nucleic Acids Res. 36, D651-655 (2008)

DIMA-the domain interaction map has evolved from a simple web server for domain phylogenetic profiling into an integrative prediction resource combining both experimental data on domain-domain interactions and predictions from two different algorithm

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c0decb922c968bfa034485acff1596bb
http://europepmc.org/articles/PMC2238836

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Prediction of human protein-protein interaction by a domain-based approach

Autor: Shan Chang, Xiaopan Zhang, Jie Song, Xiong Jiao

Publikováno v: Journal of theoretical biology. 396

Protein–protein interactions (PPIs) are vital to a number of biological processes. With computational methods, plenty of domain information can help us to predict and assess PPIs. In this study, we proposed a domain-based approach for the predictio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b81e5ee6132382f4f3e1ea75392d22f
https://pubmed.ncbi.nlm.nih.gov/26925814

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3did: interacting protein domains of known three-dimensional structure

Autor: Robert Bruce Russell, Patrick Aloy, Amelie Stein

Publikováno v: Nucleic Acids Research

The database of 3D Interacting Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details neces

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::07b751590fe694ebcc0a31b39a046930
http://europepmc.org/articles/PMC539991

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DDI2PPI

Autor: Cathy H. Wu, Tianchuan Du, Qinghua Wang, Alvaro J. González, Hongzhan Huang, Li Liao

Publikováno v: BCB

Protein-protein interactions (PPIs) play essential roles in many biological processes. The large gap between the fast growing protein sequence information and the experimentally verified PPI information has motivated the development of computational

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1a98ab682da1667a7be8bfb3bf52c694
https://doi.org/10.1145/2649387.2660814

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