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SuperTarget and Matador: resources for exploring drug-target relationships

S. Gunther, M. Kuhn, M. Dunkel, M. Campillos, C. Senger, E. Petsalaki, J. Ahmed, E. G. Urdiales, A. Gewiess, L. J. Jensen, R. Schneider, R. Skoblo (+4 others)
2007 Nucleic Acids Research  
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

Michael Kuhn, Mónica Campillos, Paula González, Lars Juhl Jensen, Peer Bork
2008 FEBS Letters  
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

Ya-Zhou Sun, De-Hong Zhang, Shu-Bin Cai, Zhong Ming, Jian-Qiang Li, Xing Chen
2018 Frontiers in Cellular and Infection Microbiology  
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

M. Kuhn, C. von Mering, M. Campillos, L. J. Jensen, P. Bork
2007 Nucleic Acids Research  
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

Tiejun Cheng, Ming Hao, Takako Takeda, Stephen H. Bryant, Yanli Wang
2017 AAPS Journal  
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

Anna Cichonska, Juho Rousu, Tero Aittokallio
2015 Expert Opinion on Drug Discovery  
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

Liang-Chin Huang, Ergin Soysal, W Zheng, Zhongming Zhao, Hua Xu, Jingchun Sun
2015 BMC Systems Biology  
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

Jing Zhao, Jian Yang, Saisai Tian, Weidong Zhang
2019 Quantitative Biology  
, 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

Liqian Zhou, Zejun Li, Jialiang Yang, Geng Tian, Fuxing Liu, Hong Wen, Li Peng, Min Chen, Ju Xiang, Lihong Peng
2019 Molecules  
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

Yang Li, Yu-An Huang, Zhu-Hong You, Li-Ping Li, Zheng Wang
2019 Molecules  
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

Neha Choudhary, Vikram Singh, Hiroyoshi Ariga
2018 PLoS ONE  
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

Tamer N. Jarada, Jon G. Rokne, Reda Alhajj
2020 Journal of Cheminformatics  
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

Gerry Maggiora, Vijay Gokhale
2017 F1000Research  
.: 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

Krisztian Buza, Ladislav Peška, Júlia Koller, Hans A Kestler
2020 PLoS ONE  
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

Olga V. Kalinina, Oliver Wichmann, Gordana Apic, Robert B. Russell, Roland L. Dunbrack
2011 PLoS Computational Biology  
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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