PharmMapper protocols

View PharmMapper computational protocol

PharmMapper statistics

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PharmMapper specifications


Unique identifier OMICS_13721
Name PharmMapper
Interface Web user interface
Restrictions to use None
Input data A file with single drug-like molecule or natural product stored in Tripos Mol2 or MDL SDF
Output data A ranked list of hit target pharmacophore models that are sorted by fit score in descending order
Programming languages PHP, Python
Database management system MySQL
Computer skills Basic
Stability No
Maintained No



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Publications for PharmMapper

PharmMapper in pipeline

PMCID: 4992511
PMID: 27579049
DOI: 10.1155/2016/7379146

[…] that these three protein functions were inseparable from the pharmacological actions of jgt., to study the relationship between the compounds and the predicted pathways and targets, we applied the pharmmapper database, kegg database, and cytoscape software to integrate the network pharmacology. eventually, 28 predicted targets and 17 primary pathways related to the inflammatory response […]

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PharmMapper in publications

PMCID: 5884779
PMID: 29618826
DOI: 10.1038/s41598-018-21515-6

[…] online databases including tcm [email protected] (tdt) and tcm-sp databases. for 229 potential target proteins for liuweiwuling, the putative targets of these compounds might act on were predicted by pharmmapper via a molecular docking method towards the known human proteins ( only the targets with fit score more than 4.0 were reserved. in summary, the approach […]

PMCID: 5877757
PMID: 29562629
DOI: 10.3390/ijms19030896

[…] and the contour map of around 77 compounds; the topomer comfa and comsia models were reliable with the statistical data. the protein–protein interaction network was constructed by combining the pharmmapper platform and string database. after generating the sub-network, the phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (pik3ca with protein data bank id: 3zim) […]

PMCID: 5859839
PMID: 29692855
DOI: 10.1155/2018/5059743

[…] information attached to the chemical abstracts service; and get the molecular structure of each active compound. draw them in chembiodraw and save as “mol2” file format. import these files into pharmmapper (, which is a web server for potential drug-target identification using pharmacophore mapping approach []., acquire associated known target proteins […]

PMCID: 5840524
PMID: 29551975
DOI: 10.3389/fphar.2018.00165

[…] comprehensive approach of information integration, chemometric method and text-mining was introduced to discover the targets of xshg. firstly, the most likely biological targets were retrieved from pharmmapper sever (), stitch, and sea (; ; ). afterward, the candidate bioactive ingredients were imported to google scholar, drugbank, ttd, and herbal ingredients targets database (hit) () […]

PMCID: 5829364
PMID: 29619072
DOI: 10.1155/2018/6517034

[…] these chemicals after deleting the replicate data. eventually, 43 herbal compounds with structural information were reserved for further study. we imported these 3d molecular structure files into pharmmapper [] (, which is an online server that exploits pharmacophore mapping approach for potential drug target identification. the compounds without […]

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PharmMapper institution(s)
Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, China; School of Information Science and Engineering, East China University of Science and Technology, Shanghai, China; Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
PharmMapper funding source(s)
Major State Basic Research Project (grants 2009CB918501 and 2009CB918502); National Natural Science Foundation of China (grants 20803022 and 20721003); Shanghai Committee of Science and Technology (grants 09dZ1975700 and 08JC1407800); 863 Hi-Tech Program of China (grants 2007AA02Z304 and 2007AA02Z330); Major National Scientific and Technological Project of China (grants 2009ZX09501-001 and 2009ZX09301-001); 111 Project (grant B07023); Shanghai Rising-Star Program (grant 10QA1401800)

PharmMapper review

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Andrew Miller

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Very intuitive platform for drug target analysis