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SuperTarget and Matador: resources for exploring drug-target relationships
2007
Nucleic Acids Research
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SuperTarget and Matador are available at ...
Furthermore, we provide tools for 2D drug screening and sequence comparison of the targets. ...
Hossbach and I. Jaeger for assistance during literature screening, software testing and improvement of the web interface. Furthermore, we thank M. ...
doi:10.1093/nar/gkm862
pmid:17942422
pmcid:PMC2238858
fatcat:lvnaeh7vonhylj72jjem4l2ztu
Large-scale prediction of drug-target relationships
2008
FEBS Letters
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Here we review recent attempts to apply large-scale computational analyses to predict novel interactions of drugs and targets from molecular and cellular features. ...
The integration of relevant data does not only allow analyses at the network level, but also provides a more global view on drug-target relations. ...
We thank Paul Hawkins and Bob Tolbert from OpenEye Scientific Software for providing the shape comparisons of chemical structures. This work was funded by the BMBF QuantPro Grant (0313831D). ...
doi:10.1016/j.febslet.2008.02.024
pmid:18291108
fatcat:3of56tx5wvavvais7u66h5mtum
MDAD: A Special Resource for Microbe-Drug Associations
2018
Frontiers in Cellular and Infection Microbiology
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A high-quality comprehensive microbe and drug association database will be extremely beneficial to explore the relationship between them. ...
We hope MDAD will be a useful resource for deeper understanding of microbe and drug interactions and will also be beneficial to drug design, disease therapy and human health. ...
ACKNOWLEDGMENTS We thank reviewers for their valuable suggestions. ...
doi:10.3389/fcimb.2018.00424
pmid:30581775
pmcid:PMC6292923
fatcat:tarccikd7revhiw7i3iass6g7y
STITCH: interaction networks of chemicals and proteins
2007
Nucleic Acids Research
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To facilitate access to this data, STITCH ('search tool for interactions of chemicals') integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target ...
relationships. ...
ACKNOWLEDGEMENTS The authors thank members of the Bork and von Mering groups for comments on the STITCH web interface. This work was funded by the BMBF QuantPro grant (0313831D). ...
doi:10.1093/nar/gkm795
pmid:18084021
pmcid:PMC2238848
fatcat:uplvdvv2wzcjfntakzns7ctgki
Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review
2017
AAPS Journal
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We also summarize popular public data resources and online tools for DTI prediction. ...
of drug molecules across multiple biological targets, and druginduced gene expressions. ...
various information resources for drugs, compounds, and knowledge about their therapeutic targets. ...
doi:10.1208/s12248-017-0092-6
pmid:28577120
fatcat:7bfu7b7mbran7lkhjuwblsjgzq
Identification of drug candidates and repurposing opportunities through compound–target interaction networks
2015
Expert Opinion on Drug Discovery
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Janica Wakkinen and Dr. Simon Anders for many useful discussions about different types of experimental assays and computational models. ...
www.drugkinet.ca TTD [88] Information on the therapeutic targets http://bidd.nus.edu.sg/group/ttd SuperTarget [89] Drug--target interactions http://insilico.charite.de/supertarget MATADOR [89] Data ...
, and other resources. ...
doi:10.1517/17460441.2015.1096926
pmid:26429153
fatcat:vtz37pji6jcnlmcuw6k3v7t3kq
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case
2015
BMC Systems Biology
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Results: In this study, we created a weighted and integrated drug-target interactome (WinDTome) to provide a comprehensive resource of drug-target associations for computational pharmacology. ...
We first collected drug-target interactions from six commonly used drug-target centered data sources including DrugBank, KEGG, TTD, MATADOR, PDSP K i Database, and BindingDB. ...
Kevin Zhu for helping us to clean the intervention terms in clinical trial data. This project was partly supported by a 2013 NARSAD ...
doi:10.1186/1752-0509-9-s4-s2
pmid:26100720
pmcid:PMC4474536
fatcat:jtkwqtlcfza3zkb7354cmbtf2e
A survey of web resources and tools for the study of TCM network pharmacology
2019
Quantitative Biology
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, web servers for the prediction of drug targets, and tools for network and functional analysis. ...
Years of research in related fields has developed many databases and tools that are useful for the study of TCM network pharmacology. In this paper, we introduce some of such free resources. ...
Currently, the paradigm of "multi-target drug discovery" based on molecular network is becoming a new trend, and drug discovery tends to get resources and inspiration from traditional drugs and folk medicines ...
doi:10.1007/s40484-019-0167-8
fatcat:2d2o5o4b3zd75jntnmof3pi4gu
Revealing Drug-Target Interactions with Computational Models and Algorithms
2019
Molecules
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Identifying possible drug-target interactions (DTIs) has become an important task in drug research and development. ...
Methods: We introduced relevant databases and packages, mainly provided a comprehensive review of computational models for DTI identification, including network-based algorithms and machine learning-based ...
In addition, SuperTarget provides 282 drug-target-related pathways, 6532 drug-target-related ontologies, and 63 cytochromes. ...
doi:10.3390/molecules24091714
fatcat:327feax5tvhsxccza47g3we75e
Drug-Target Interaction Prediction Based on Drug Fingerprint Information and Protein Sequence
2019
Molecules
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We finally combine the features of drugs and protein together to represent features of each drug-target pair and use a rotation forest classifier to calculate the scores of interaction possibility, for ...
We anticipate that the proposed method can be used as an effective tool for predicting drug-target interactions on a large scale, given the information of protein sequences and drug fingerprints. ...
-H.Y. for their valuable suggestions.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/molecules24162999
pmid:31430892
pmcid:PMC6719962
fatcat:osxzl5h4vrhqflsomvo5ctahsu
A census of P. longum's phytochemicals and their network pharmacological evaluation for identifying novel drug-like molecules against various diseases, with a special focus on neurological disorders
2018
PLoS ONE
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role in diseases, and (iii) reported several novel drug targets. ...
other diseases and can also be applied to scrutinize other indigenous herbs for drug-design studies. ...
Acknowledgments N.C. and V.S. thank the Central University of Himachal Pradesh for providing computational infrastructure. ...
doi:10.1371/journal.pone.0191006
pmid:29320554
pmcid:PMC5761900
fatcat:bcvcdx5n2zgq3hbe2xrcvh45lu
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions
2020
Journal of Cheminformatics
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Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs and discovering therapies for untreated diseases. ...
First, we highlight different drug repositioning strategies and provide an overview of frequently used resources. ...
RDRD provides a comprehensive resource for developing targeted effective therapies for rare disease patients. ...
doi:10.1186/s13321-020-00450-7
pmid:33431024
fatcat:yymhfsis4vgibo4surxzcrvp5m
A simple mathematical approach to the analysis of polypharmacology and polyspecificity data
2017
F1000Research
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.: SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res. 2008; 36(Database issue): D919-D922. PubMed Abstract | Publisher Full Text | Free Full Text 33. ...
.: GESSE: Predicting drug side effects from drug-target relationships. J Chem Inf Model. 2015; 55(9): 1804-1823. PubMed Abstract | Publisher Full Text 8. ...
Acknowledgments GM wishes to thank Professor Jürgen Bajorath and Dr. ...
doi:10.12688/f1000research.11517.1
pmid:28690829
pmcid:PMC5482344
fatcat:c3sz3e2m3fhzndkwzyclhjufnm
Modified linear regression predicts drug-target interactions accurately
2020
PLoS ONE
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State-of-the-art approaches for the prediction of drug-target interactions (DTI) are based on various techniques, such as matrix factorisation, restricted Boltzmann machines, network-based inference and ...
We evaluate our approach on publicly available real-world drug-target interaction datasets. ...
Gü nther Stefan and Kuhn Michael and Dunkel Mathias and Campillos Monica and Senger Christian and Petsalaki et al. SuperTarget and Matador: resources for exploring drug-target relationships. ...
doi:10.1371/journal.pone.0230726
pmid:32251481
fatcat:vmcm5siznrb2vdzqkqa5ek4omu
Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs
2011
PLoS Computational Biology
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Biological networks are powerful tools for predicting undocumented relationships between molecules. ...
Within 19,578 novel predicted interactions are 7,793 involving 718 drugs, including filaminast, coumarin, alitretonin and erlotinib. ...
Acknowledgments We thank Anne-Claude Gavin and Peer Bork (both at EMBL, Heidelberg) for a critical reading of the manuscript. ...
doi:10.1371/journal.pcbi.1002043
pmid:21573205
pmcid:PMC3088657
fatcat:xdqsxlfp5jdtzgev7b33hqgkfy
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