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drugCIPHER specifications

Information


Unique identifier OMICS_13138
Name drugCIPHER
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data Drug Therapeutic Similarity, Drug Chemical Similarity, known drug-target interactions, the PPI network
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Shao Li <>

Publication for drugCIPHER

drugCIPHER in publications

 (11)
PMCID: 5872392
PMID: 29589568
DOI: 10.1186/s12911-018-0592-z

[…] methods to predict herbal protein targets. on the other hand, plenty of prediction approaches based on network propagation have been widely applied to identify genetic associations, e.g., drugcipher-ms [] for drug target identification, prince [], pgwalk [] and know-gene [] for disease gene identification and herb target prediction, which indicated that network propagation […]

PMCID: 5790780
PMID: 29434546
DOI: 10.3389/fphar.2018.00010

[…] perform a functional analysis of matrine, a marketed drug in china extracted from a medical herb ku-shen (radix sophorae flavescentis). here, the network target of matrine was firstly predicted by drugcipher, a genome-wide target prediction method. based on the network target of matrine, we performed a functional gene set enrichment analysis to computationally identify the potential […]

PMCID: 5647051
PMID: 28849026
DOI: 10.3892/mmr.2017.7287

[…] weightlessness induced muscle atrophy. the results indicated that bz could significantly protect muscles from simulated weightlessness-induced atrophy. to elucidate the underlying mechanisms, drugcipher-cs methods were introduced to predict its potential targets, significantly enriched pathways and biological processes. the results demonstrated that the calcium signaling pathway, citrate […]

PMCID: 4427773
PMID: 26060814
DOI: 10.1155/2015/239654

[…] to the one targeted by a drug, this protein is more likely to be targeted by the drug or a drug with similar therapeutic effects. based on this idea, zhao and li [] proposed a novel method named drugcipher to predict drug-target interactions by integrating drug therapy information, chemical structure information, and ppin. later, drugcipher has been successfully applied to predict targets […]

PMCID: 4423032
PMID: 25983850
DOI: 10.1155/2015/451319

[…] combinational rules, achieving a good balance among the herb's frequency, independence, and distance in herbal formulae []., target prediction for herbal compounds and herbs. in the present study, drugcipher, a method we developed previously [], is used to predict the target profile for all available compounds collected from each herb in the core herb networks. drugcipher is a regression model […]


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drugCIPHER institution(s)
MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, China
drugCIPHER funding source(s)
This work is supported by the National Natural Science Foundation of China (Nos. 60934004, 30873464 and 60721003).

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