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Predicting target p...
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Ahmed, LaeeqKTH,Beräkningsvetenskap och beräkningsteknik (CST),Royal Inst Technol KTH, Dept Elect Engn & Computat Sci, Lindstedtsvagen 5, S-10044 Stockholm, Sweden.
(author)
Predicting target profiles with confidence as a service using docking scores
- Article/chapterEnglish2020
Publisher, publication year, extent ...
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2020-10-15
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Springer Nature,2020
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printrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:kth-285717
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https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-285717URI
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https://doi.org/10.1186/s13321-020-00464-1DOI
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-424040URI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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QC 20201126
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Background: Identifying and assessing ligand-target binding is a core component in early drug discovery as one or more unwanted interactions may be associated with safety issues. Contributions: We present an open-source, extendable web service for predicting target profiles with confidence using machine learning for a panel of 7 targets, where models are trained on molecular docking scores from a large virtual library. The method uses conformal prediction to produce valid measures of prediction efficiency for a particular confidence level. The service also offers the possibility to dock chemical structures to the panel of targets with QuickVina on individual compound basis. Results: The docking procedure and resulting models were validated by docking well-known inhibitors for each of the 7 targets using QuickVina. The model predictions showed comparable performance to molecular docking scores against an external validation set. The implementation as publicly available microservices on Kubernetes ensures resilience, scalability, and extensibility.
Subject headings and genre
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Alogheli, HibaUppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)hibhu475
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Arvidsson Mc Shane, StaffanUppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)staar541
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Alvarsson, Jonathan,1981-Uppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)jonal195
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Berg, ArvidUppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)arvbe873
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Larsson, AndersUppsala universitet,Institutionen för farmaceutisk biovetenskap,Institutionen för cell- och molekylärbiologi,nbis - national bioinformatics infrastructure sweden(Swepub:uu)andla958
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Schaal, Wesley,PhDUppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)weslscha
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Laure, ErwinKTH,Beräkningsvetenskap och beräkningsteknik (CST),Royal Inst Technol KTH, Dept Elect Engn & Computat Sci, Lindstedtsvagen 5, S-10044 Stockholm, Sweden.(Swepub:kth)u1n9d88r
(author)
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Spjuth, Ola,Docent,1977-Uppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)olspj499
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KTHBeräkningsvetenskap och beräkningsteknik (CST)
(creator_code:org_t)
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In:Journal of Cheminformatics: Springer Nature12:11758-2946
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Ahmed, Laeeq
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Alogheli, Hiba
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Arvidsson Mc Sha ...
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Alvarsson, Jonat ...
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Berg, Arvid
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Larsson, Anders
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Schaal, Wesley, ...
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Laure, Erwin
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Spjuth, Ola, Doc ...
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- MEDICAL AND HEALTH SCIENCES
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NATURAL SCIENCES
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Journal of Chemi ...
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Royal Institute of Technology
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Uppsala University