ChemMapper protocols

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ChemMapper specifications

Information


Unique identifier OMICS_03423
Name ChemMapper
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability No
Maintained No

Subtool


  • SHAFTS

Maintainer


This tool is not available anymore.

Additional information


ChemMapper implements SHAFTS, a fast 3D similarity method in which the 3D similarity calculation is driven by the hybrid information of molecular shape and chemotype features.

Publications for ChemMapper

ChemMapper in pipelines

 (2)
2017
PMCID: 5432314
PMID: 28212580
DOI: 10.18632/oncotarget.15351

[…] of the chemical ingredients. the validated targets were extracted from the herbal ingredients’ targets (hit) database [] (http://lifecenter.sgst.cn/hit/). the predicted targets were obtained using chemmapper [] (http://lilab.ecust.edu.cn/chemmapper/), an online tool for predicting targets based on 3d similarity., ten herbs (cervus nippon temminck (nt), ginger charcoal (gc), citri reticulatae […]

2016
PMCID: 5008533
PMID: 27583849
DOI: 10.1097/MD.0000000000004389

[…] targets of the chemical ingredients. the validated targets were extracted from the herbal ingredients’ targets database[] (http://lifecenter.sgst.cn/hit/). the predicted targets were obtained using chemmapper[] (http://lilab.ecust.edu.cn/chemmapper/), an online tool for predicting targets based on 3d similarity. the scores for the validated targets were defined as 1, and the scores […]


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ChemMapper in publications

 (7)
PMCID: 5857607
PMID: 29594101
DOI: 10.3389/fchem.2018.00057

[…] 4gq4 and 4go8, respectively) were used as query (shi et al., ; he et al., ). an in-house library comprising ~1,600 existing drugs was aligned onto the query to perform 3d similarity searching using shafts (liu et al., ; lu et al., ). a set of 12 top ranked compounds with shafts similarity scores >1.2 (maximum 2.0) were selected for primary validation, which indicated that loperamide, […]

PMCID: 5766629
PMID: 29330507
DOI: 10.1038/s41598-017-18325-7

[…] the validated targets of the 4 compounds were extracted from the herbal ingredients’ targets (hit) database (http://lifecenter.sgst.cn/hit/). the predicted targets of cki were obtained using chemmapper (http://lilab.ecust.edu.cn/chemmapper/), an online tool for predicting targets based on 3d similarity. these targets were mapped to hcc-related genes to obtain the candidate targets […]

PMCID: 5476563
PMID: 28630494
DOI: 10.1038/s41598-017-04184-9

[…] the covalently modified inhibitor-kinase complexes were minimized in water solvent using macromodel application with flexible ligand and constrained protein., the scaffold hopping was conducted by shafts, . the query molecule is the docked pose of compound 9 obtained from the above docking study. the aligned pose of compound 16a (shown in fig. ) was generated by fast 3d similarity calculation […]

PMCID: 5476590
PMID: 28630414
DOI: 10.1038/s41598-017-04264-w

[…] and database molecules are generally referred to as test and training sets, respectively. there are fewer methods in the ligand-centric category and these are based on molecular similarity (e.g., chemmapper, electroshape polypharmacology server) or on the similarity of bioactivity spectra (e.g. compare). it is worth noting that not all methods employing molecular similarity […]

PMCID: 5005041
PMID: 26193243
DOI: 10.3390/molecules200712841

[…] feature, i and j are feature points. dij is a distance between feature points i and j after superimposition, and rf is a tolerance. the similarity of two molecules is given as . procedure of shafts is illustrated in ., an alternative for molecular shape description is to consider the surface of molecules. using surface representation, ligand binding can be considered as matching […]


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ChemMapper institution(s)
School of Information Science and Engineering, Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China

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