ArticleJournal of cheminformatics2014
In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion.
Article in Journal of cheminformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Review
- Enhancing the confidence of potential targets enriched by similarity-centric models: the crucial role of the similarity threshold.Frontiers in pharmacology · 2025Article
- Benchmarking reverse docking through AlphaFold2 human proteome.Protein science : a publication of the Protein Society · 2024Article
- The Immunosuppressive Properties of Cyclo-[Pharmaceutics · 2024Article
- Comprehensive survey of target prediction web servers for Traditional Chinese Medicine.Heliyon · 2023Review
- In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences.Journal of cheminformatics · 2023Article
- A comprehensive review of artificial intelligence and network based approaches to drug repurposing in Covid-19.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Review
- Inhibitors ofPharmaceuticals (Basel, Switzerland) · 2022Article
- An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph.Briefings in bioinformatics · 2022Review
- Recent Advances in In Silico Target Fishing.Molecules (Basel, Switzerland) · 2021Review
- LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds.Journal of cheminformatics · 2021Article
- Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches.Molecules (Basel, Switzerland) · 2020Review
- Cytotoxicity and Antimycobacterial Properties of Pyrrolo[1,2-Antibiotics (Basel, Switzerland) · 2020Article
- Reliable Target Prediction of Bioactive Molecules Based on Chemical Similarity Without Employing Statistical Methods.Frontiers in pharmacology · 2019Article
- Cell fishing: A similarity based approach and machine learning strategy for multiple cell lines-compound sensitivity prediction.PloS one · 2019Article
- Bioinformatics analysis of differentially expressed genes in hepatocellular carcinoma cells exposed to Swertiamarin.Journal of Cancer · 2019Article
- Toxicodynamics of Mycotoxins in the Framework of Food Risk Assessment-An In Silico Perspective.Toxins · 2018Review
- Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds.Frontiers in chemistry · 2018Review
- Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review.The AAPS journal · 2017Review
- C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLigand-based in silico target fishing can be used to identify the potential interacting target of bioactive ligands, which is useful for understanding the polypharmacology and safety profile of existing drugs. The underlying principle of the approach is that known bioactive ligands can be used as reference to predict the targets for a new compound.
resultsWe tested a pipeline enabling large-scale target fishing and drug repositioning, based on simple fingerprint similarity rankings with data fusion. A large library containing 533 drug relevant targets with 179,807 active ligands was compiled, where each target was defined by its ligand set. For a given query molecule, its target profile is generated by similarity searching against the ligand sets assigned to each target, for which individual searches utilizing multiple reference structures are then fused into a single ranking list representing the potential target interaction profile of the query compound. The proposed approach was validated by 10-fold cross validation and two external tests using data from DrugBank and Therapeutic Target Database (TTD). The use of the approach was further demonstrated with some examples concerning the drug repositioning and drug side-effects prediction. The promising results suggest that the proposed method is useful for not only finding promiscuous drugs for their new usages, but also predicting some important toxic liabilities.
conclusionsWith the rapid increasing volume and diversity of data concerning drug related targets and their ligands, the simple ligand-based target fishing approach would play an important role in assisting future drug design and discovery.
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