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PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach

Xiaofeng Liu, Sisheng Ouyang, Biao Yu, Yabo Liu, Kai Huang, Jiayu Gong, Siyuan Zheng, Zhihua Li, Honglin Li, Hualiang Jiang
2010 Nucleic Acids Research  
SUMMARY We presented here the first web server for potential drug targets identification via large-scale reverse pharmacophore mapping strategy.  ...  Herein, we present the first web-based tool PharmMapper for potential drug target prediction against any given small molecules via a 'reverse' pharmacophore mapping approach.  ... 
doi:10.1093/nar/gkq300 pmid:20430828 pmcid:PMC2896160 fatcat:i4dq7sv7araglncppme5tgu4gm

PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database

Xia Wang, Yihang Shen, Shiwei Wang, Shiliang Li, Weilin Zhang, Xiaofeng Liu, Luhua Lai, Jianfeng Pei, Honglin Li
2017 Nucleic Acids Research  
The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database.  ...  In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores.  ...  DISCUSSION PharmMapper is an open-source web server that identifies potential drug targets via large-scale reverse pharmacophore mapping strategy.  ... 
doi:10.1093/nar/gkx374 pmid:28472422 pmcid:PMC5793840 fatcat:amn26acpsncfpjva22uvwp6q5u

The discovery of a novel inhibitor of apoptotic protease activating factor-1 (Apaf-1) for ischemic heart: synthesis, activity and target identification

Ying Wang, Yang Cao, Qing Zhu, Xianfeng Gu, Yi Zhun Zhu
2016 Scientific Reports  
Liu, X., et al., PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucleic acids research, 2010. 38(suppl 2): p. W609-W614.  ...  The predicted target candidates for kinases of compound ZYZ-488 using PharmMapper server [1] .. Table S1 .  ... 
doi:10.1038/srep29820 pmid:27443636 pmcid:PMC4957240 fatcat:ox3tyh6h5ve57gjjml773s2gti

Identification of a Potential Target of Capsaicin by Computational Target Fishing

Xuan-yi Ye, Qing-zhi Ling, Shao-jun Chen
2015 Evidence-Based Complementary and Alternative Medicine  
In the present study, the potential targets of capsaicin were predicted using PharmMapper and confirmed via chemical-protein interactome (CPI) and molecular docking.  ...  Carbonic anhydrase 2 was identified as the main disease-related target, with the pharmacophore model matching well with the molecular features of capsaicin.  ...  Methods Targets Predicted by PharmMapper. PharmMapper is a web server for potential drug target identification based on the use of a pharmacophore mapping approach [12] .  ... 
doi:10.1155/2015/983951 pmid:26770256 pmcid:PMC4681817 fatcat:cu3wdbz4rrcidlnbod6gg3fize

Modeling Analysis of Potential Target of Dolastatin 16 by Computational Virtual Screening

Ting-Ting Liang, Qi Zhao, Shan He, Fang-Zhou Mu, Wei Deng, Bing-Nan Han
2018 Chemical and pharmaceutical bulletin  
In this study, peptidyl-prolyl cis-trans isomerase FKBP1A (FKBP12) was predicted as a potential target of dolastatin 16 via PharmMapper as well as verified using chemical-protein interactome (CPI) and  ...  FKBP1A has been previously identified as a target for the natural polyketide FK506 (tacrolimus), an immune suppressor inhibiting the rejection of organ transplantation in clinical use.  ...  Experimental Targets Predicted by PharmMapper PharmMapper is a freely accessed web server that uses a pharmacophore mapping approach to identify potential target candidates for the given probe small molecules  ... 
doi:10.1248/cpb.c17-00966 pmid:29863061 fatcat:u7z2uisg2bd5dhjxtllez4mhsi

Identification of neprilysin as a potential target of arteannuin using computational drug repositioning

Xuan-Yi Ye, Qing-Zhi Ling, Shao-Jun Chen
2017 Brazilian Journal of Pharmaceutical Sciences  
In this study, the reverse docking server PharmMapper was used to identify potential targets of arteannuin.  ...  The chemical-protein interactome and docking results agreed with those of PharmMapper, further implicating neprilysin as a potential target.  ...  MATERIALS AND METHODS Target prediction by PharmMapper PharmMapper (http://59.78.96.61/pharmmapper) is a web server for identification of potential drug targets that utilises a large-scale reverse pharmacophore  ... 
doi:10.1590/s2175-97902017000216087 fatcat:ke43lxfhwndebbisp4dht3aiza

A Potential Target of Tanshinone IIA for Acute Promyelocytic Leukemia Revealed by Inverse Docking and Drug Repurposing

Shao-Jun Chen
2014 Asian Pacific Journal of Cancer Prevention  
In this research, PharmMapper server was used as the inverse docking tool andnd the results were verified by Autodock vina in PyRx 0.8, and by DRAR-CPI, a server for drug repositioning via the chemical-protein  ...  These results indicated that RARα may be a potential target of Tanshinone IIA for APL. The study can provide useful information for further biological and biochemical research on natural compounds.  ...  Materials and Methods Protein target prediction by PharmMapper Pharm Mapper server is a web server for potential drug target identification using pharmacophore mapping approach (Liu et al., 2010) .  ... 
doi:10.7314/apjcp.2014.15.10.4301 fatcat:tvvcnzfu3vak3pfhepnaq2cx7m

Identification of a Potential Anticancer Target of Danshensu by Inverse Docking

Shao-Jun Chen, Ji-Long Ren
2014 Asian Pacific Journal of Cancer Prevention  
This approach can provide useful information for studying pharmacological effects of agents of interest.  ...  Method: PharmMapper and idTarget servers were used as tools, and the results were checked with the molecular docking program autodock vina in PyRx 0.8.  ...  target candidates for the given probe small molecules (drugs, natural products or other newly discovered compounds with binding target unidentified) using pharmacophore mapping approach (Liu et al.,  ... 
doi:10.7314/apjcp.2014.15.1.111 fatcat:tt3ukgtbjzbdtbd4gr4f6ih4xa

iDrug: a web-accessible and interactive drug discovery and design platform

Xia Wang, Haipeng Chen, Feng Yang, Jiayu Gong, Shiliang Li, Jianfeng Pei, Xiaofeng Liu, Hualiang Jiang, Luhua Lai, Honglin Li
2014 Journal of Cheminformatics  
Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well.  ...  The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g.  ...  Target identification iDrug uses the reverse pharmacophore mapping procedure to predict potential drug targets.  ... 
doi:10.1186/1758-2946-6-28 pmid:24955134 pmcid:PMC4046018 fatcat:zeu54az7wfeerk5reebpxrjmmq

Systematic Understanding of the Mechanism of Salvianolic Acid A via Computational Target Fishing

Shao-Jun Chen, Ming-Chao Cui
2017 Molecules  
In the present study, the druggability of SAA was measured using the TCMSP server, and potential targets of SAA were identified by PharmMapper and DRAR-CPI.  ...  Intersecting targets were then assessed by GeneMANIA and GO pathway analysis, and drug-target-pathway networks were constructed to give a visual view.  ...  Computational Target Fishing by PharmMapper and DRAR-CPI PharmMapper, a reverse docking server, can identify potential protein targets for small molecule compounds via a pharmacophore mapping approach  ... 
doi:10.3390/molecules22040644 pmid:28420179 fatcat:xydz3ticifbtziitnu5wlqmkqe

ANALYSIS OF NEW POLYFLUOROTHIOACYLATED AMINO ACIDS DERIVATIVES BY IN SILICO AND IN VITRO METHODS

К. C. Науменко, A. В. Головань, Г. В. Баранова, Ю. Г. Шермолович, Н. В. Пікун, С. Д. Загородня
2017 Mìkrobìologìâ ì Bìotehnologìâ  
PASS software, web-server PharmMapper, PCR, MTT assay, trypan blue and neutral red assay were used. Results.  ...  Several targets were identified by using molecular docking (PharmMapper).  ...  PharmMapper is a web server for identification of potential drug target based on the use of a pharmacophore mapping approach.  ... 
doi:10.18524/2307-4663.2017.4(40).118939 fatcat:d5h6hkf6xvfmvbadhjscau6w7e

Uncovering the action mechanism of polydatin via network pharmacological target prediction

Boyu Pan, Yuanyuan Ren, Liren Liu
2018 RSC Advances  
Polydatin (PD), a small natural compound originally extracted from Polygonum cuspidatum, exerts distinct biological functions in a variety of diseases.  ...  using pharmacophore mapping approach. 46 For a given compound, it can provide the top 300 targets, sorted by t score in descending order.  ...  Identication of potentially drug targets by PharmMapper and ChemMapper PharmMapper, as a reverse docking server, can identify the potentially protein target candidates for the given probe small molecules  ... 
doi:10.1039/c8ra03124j pmid:35539671 pmcid:PMC9080635 fatcat:66j6cr5n4rd7bhpnsr7csky4wa

Reverse pharmacophore mapping and molecular docking studies for discovery of GTPase HRas as promising drug target for bis-pyrimidine derivatives

Sanjiv Kumar, Jagbir Singh, Balasubramanian Narasimhan, Syed Adnan Ali Shah, Siong Meng Lim, Kalavathy Ramasamy, Vasudevan Mani
2018 Chemistry Central Journal  
An open web server PharmMapper was used to identify the possible target of the developed compounds through reverse pharmacophore mapping.  ...  PharmMapper, a robust online tool was used for identifying the target proteins based on reverse pharmacophore mapping.  ...  Acknowledgements The authors are thankful to Head, Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, for providing necessary facilities to carry out this research work.  ... 
doi:10.1186/s13065-018-0475-5 pmid:30345469 pmcid:PMC6768019 fatcat:xnbndoleh5gqjet35a4ivv2tjy

Antiviral and apoptosis modulating potential of fluorinated derivatives of uracil

Krystyna Naumenko, Anna Golovan, Lubov Zelena, Yuriy Shermolovich, Gudz Ganna, Svіtlana Zagorodnya
2018 ScienceRise Biological Science  
PharmMapper is a web server for potential drug target identification based on the use of a pharmacophore mapping approach.  ...  The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database.  ... 
doi:10.15587/2519-8025.2018.124689 fatcat:ngptivx3ejerhbpfxzjellzmle

Recent Advances in In Silico Target Fishing

Salvatore Galati, Miriana Di Stefano, Elisa Martinelli, Giulio Poli, Tiziano Tuccinardi
2021 Molecules  
For these reasons, target fishing has increasingly become a key approach for polypharmacology, drug repurposing, and the identification of new drug targets.  ...  In silico target fishing, whose aim is to identify possible protein targets for a query molecule, is an emerging approach used in drug discovery due its wide variety of applications.  ...  Another widespread tool is PharmMapper, a freely accessible web server for target identification based on the pharmacophore mapping procedure [121] .  ... 
doi:10.3390/molecules26175124 pmid:34500568 fatcat:jmz5qvhosjcg7jyey4rzbpuvce
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