Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
Publication Date
October 07, 2016
Journal
PLOS Computational Biology
Authors
Hansaim Lim, Aleksandar Poleksic, Yuan Yao, Hanghang Tong, et al
Volume
12
Issue
10
Pages
e1005135
DOI
https://dx.plos.org/10.1371/journal.pcbi.1005135
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1005135
Web of Science
000387660200020
Scopus
84994120845
Mendeley
http://www.mendeley.com/research/largescale-offtarget-identification-using-fast-accurate-dual-regularized-oneclass-collaborative-filt
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Mendeley | Further Information

{"title"=>"Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing", "type"=>"journal", "authors"=>[{"first_name"=>"Hansaim", "last_name"=>"Lim", "scopus_author_id"=>"57191846210"}, {"first_name"=>"Aleksandar", "last_name"=>"Poleksic", "scopus_author_id"=>"8626396900"}, {"first_name"=>"Yuan", "last_name"=>"Yao", "scopus_author_id"=>"57191851460"}, {"first_name"=>"Hanghang", "last_name"=>"Tong", "scopus_author_id"=>"7201360533"}, {"first_name"=>"Di", "last_name"=>"He", "scopus_author_id"=>"57191844372"}, {"first_name"=>"Luke", "last_name"=>"Zhuang", "scopus_author_id"=>"57191835931"}, {"first_name"=>"Patrick", "last_name"=>"Meng", "scopus_author_id"=>"57191837609"}, {"first_name"=>"Lei", "last_name"=>"Xie", "scopus_author_id"=>"37002340900"}], "year"=>2016, "source"=>"PLoS Computational Biology", "identifiers"=>{"scopus"=>"2-s2.0-84994120845", "pmid"=>"27716836", "sgr"=>"84994120845", "doi"=>"10.1371/journal.pcbi.1005135", "issn"=>"15537358", "pui"=>"613093683"}, "id"=>"5ffff583-062c-33e4-8f45-e92a081fce76", "abstract"=>"Target-based screening is one of the major approaches in drug discovery. Besides the intended target, unexpected drug off-target interactions often occur, and many of them have not been recognized and characterized. The off-target interactions can be responsible for either therapeutic or side effects. Thus, identifying the genome-wide off-targets of lead compounds or existing drugs will be critical for designing effective and safe drugs, and pro-viding new opportunities for drug repurposing. Although many computational methods have been developed to predict drug-target interactions, they are either less accurate than the one that we are proposing here or computationally too intensive, thereby limiting their capability for large-scale off-target identification. In addition, the performances of most machine learning based algorithms have been mainly evaluated to predict off-target inter-actions in the same gene family for hundreds of chemicals. It is not clear how these algo-rithms perform in terms of detecting off-targets across gene families on a proteome scale. Here, we are presenting a fast and accurate off-target prediction method, REMAP, which is based on a dual regularized one-class collaborative filtering algorithm, to explore continu-ous chemical space, protein space, and their interactome on a large scale. When tested in a reliable, extensive, and cross-gene family benchmark, REMAP outperforms the state-of-the-art methods. Furthermore, REMAP is highly scalable. It can screen a dataset of 200 thousands chemicals against 20 thousands proteins within 2 hours. Using the recon-structed genome-wide target profile as the fingerprint of a chemical compound, we pre-dicted that seven FDA-approved drugs can be repurposed as novel anti-cancer therapies. The anti-cancer activity of six of them is supported by experimental evidences. Thus, REMAP is a valuable addition to the existing in silico toolbox for drug target identification,", "link"=>"http://www.mendeley.com/research/largescale-offtarget-identification-using-fast-accurate-dual-regularized-oneclass-collaborative-filt", "reader_count"=>37, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>3, "Other"=>2, "Student > Master"=>4, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>3, "Other"=>2, "Student > Master"=>4, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Biochemistry, Genetics and Molecular Biology"=>6, "Medicine and Dentistry"=>5, "Agricultural and Biological Sciences"=>10, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>5, "Chemistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>8}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>5}}, "reader_count_by_country"=>{"Hungary"=>1, "United States"=>1, "Brazil"=>1}, "group_count"=>2}

Scopus | Further Information

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