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dc.contributor.authorDönmez, Ataberk
dc.contributor.authorRifaioğlu, Ahmet Süreyya
dc.contributor.authorAcar, Aybar
dc.contributor.authorDoğan, Tunca
dc.contributor.authorAtalay, Rengül Çetin
dc.contributor.authorAtalay, Volkan
dc.date.accessioned2021-07-08T10:36:27Z
dc.date.available2021-07-08T10:36:27Z
dc.date.issued2020en_US
dc.identifier.citationDonmez, A., Rifaioglu, A. S., Acar, A., Doğan, T., Cetin-Atalay, R., & Atalay, V. (2020). iBioProVis: interactive visualization and analysis of compound bioactivity space. Bioinformatics (Oxford, England), 36(14), 4227–4230. https://doi.org/10.1093/bioinformatics/btaa496en_US
dc.identifier.urihttps://doi.org/10.1093/bioinformatics/btaa496
dc.identifier.urihttps://hdl.handle.net/20.500.12508/1855
dc.description.abstractiBioProVis is an interactive tool for visual analysis of the compound bioactivity space in the context of target proteins, drugs and drug candidate compounds. iBioProVis tool takes target protein identifiers and, optionally, compound SMILES as input, and uses the state-of-the-art non-linear dimensionality reduction method t-Distributed Stochastic Neighbor Embedding (t-SNE) to plot the distribution of compounds embedded in a 2D map, based on the similarity of structural properties of compounds and in the context of compounds' cognate targets. Similar compounds, which are embedded to proximate points on the 2D map, may bind the same or similar target proteins. Thus, iBioProVis can be used to easily observe the structural distribution of one or two target proteins' known ligands on the 2D compound space, and to infer new binders to the same protein, or to infer new potential target(s) for a compound of interest, based on this distribution. Principal component analysis (PCA) projection of the input compounds is also provided, Hence the user can interactively observe the same compound or a group of selected compounds which is projected by both PCA and embedded by t-SNE. iBioProVis also provides detailed information about drugs and drug candidate compounds through cross-references to widely used and well-known databases, in the form of linked table views. Two use-case studies were demonstrated, one being on angiotensin-converting enzyme 2 (ACE2) protein which is Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike protein receptor. ACE2 binding compounds and seven antiviral drugs were closely embedded in which two of them have been under clinical trial for Coronavirus disease 19 (COVID-19).en_US
dc.language.isoengen_US
dc.publisherNLM (Medline)en_US
dc.relation.isversionof10.1093/bioinformatics/btaa496en_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subject.classificationChemoinformatics
dc.subject.classificationVirtual Screening
dc.subject.classificationTopographic Mapping
dc.subject.classificationBiochemistry & Molecular Biology
dc.subject.classificationBiotechnology & Applied Microbiology
dc.subject.classificationComputer Science
dc.subject.classificationMathematical & Computational Biology
dc.subject.classificationMathematics
dc.subject.otherAngiotensin-converting enzyme inhibitors
dc.subject.otherAntiviral agents
dc.subject.otherBetacoronavirus
dc.subject.otherCoronavirus infections
dc.subject.otherHumans
dc.subject.otherInternet
dc.subject.otherModels
dc.subject.otherMolecular
dc.subject.otherPandemics
dc.subject.otherPeptidyl-Dipeptidase A
dc.subject.otherPneumonia
dc.subject.otherViral
dc.subject.otherPrincipal component analysis
dc.subject.otherReceptors
dc.subject.otherAdrenergic
dc.subject.otherbeta-2
dc.subject.otherReceptors
dc.subject.otherAdrenergic
dc.subject.otherbeta-3
dc.subject.otherSoftware
dc.subject.otherSpike glycoprotein
dc.subject.otherCoronavirus
dc.subject.otherUser-computer interface
dc.subject.otherADRB2 protein
dc.subject.otherHuman
dc.subject.otherADRB3 protein
dc.subject.otherAngiotensin converting enzyme 2
dc.subject.otherAntivirus agent
dc.subject.otherbeta 2 adrenergic receptor
dc.subject.otherbeta 3 adrenergic receptor
dc.subject.otherCoronavirus spike glycoprotein
dc.subject.otherDipeptidyl carboxypeptidase
dc.subject.otherDipeptidyl carboxypeptidase inhibitor
dc.subject.otherSpike protein
dc.subject.otherSARS-CoV-2
dc.subject.otherBetacoronavirus
dc.subject.otherChemistry
dc.subject.otherComputer interface
dc.subject.otherCoronavirus infection
dc.subject.otherInternet
dc.subject.otherMolecular model
dc.subject.otherPandemic
dc.subject.otherPrincipal component analysis
dc.subject.otherSoftware
dc.subject.otherVirus pneumonia
dc.titleiBioProVis: interactive visualization and analysis of compound bioactivity spaceen_US
dc.typearticleen_US
dc.relation.journalBioinformatics (Oxford, England)en_US
dc.contributor.departmentMühendislik ve Doğa Bilimleri Fakültesi -- Elektrik-Elektronik Mühendisliği Bölümüen_US
dc.identifier.volume36en_US
dc.identifier.issue14en_US
dc.identifier.startpage4227en_US
dc.identifier.endpage4230en_US
dc.relation.tubitakEEEAG-116E930
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.contributor.isteauthorRifaioğlu, Ahmet Süreyya
dc.relation.indexWeb of Science - Scopus - PubMed - TR-Dizinen_US
dc.relation.indexWeb of Science Core Collection - Science Citation Index Expanded


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