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Scaffold Hunter specifications


Unique identifier OMICS_18218
Name Scaffold Hunter
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 2.6.1
Stability Stable
Maintained Yes




No version available



  • person_outline Herbert Waldmann

Publication for Scaffold Hunter

Scaffold Hunter citations


In silico discovery of substituted pyrido[2,3 d]pyrimidines and pentamidine like compounds with biological activity in myotonic dystrophy models

PLoS One
PMCID: 5459475
PMID: 28582438
DOI: 10.1371/journal.pone.0178931

[…] space, a principal component analysis (pca) was carried out using canvas from the schrödinger 2014 suite [,], considering the radial fingerprints properties. scaffold analysis was conducted using scaffold hunter (supporting information, ) []., similarity screening was performed with the rocs tool from the openeye suite []. the chemical library was selected from a subset of the zinc database […]


Designed Spiroketal Protein Modulation

PMCID: 5435924
PMID: 28407400
DOI: 10.1002/anie.201612504

[…] by waldmann and co‐workers, , clearly placed these structures within a hierarchical classification of bioactive scaffold structures, navigable with the help of cheminformatics tools such as scaffold hunter, and inspired the design of other spiroketal libraries for phenotypic screening., , recently, 3d‐pharmacophore modelling was used to design spiroketal‐derived sugars, which showed […]


A New Set of Chemical Starting Points with Plasmodium falciparum Transmission Blocking Potential for Antimalarial Drug Discovery

PLoS One
PMCID: 4552634
PMID: 26317851
DOI: 10.1371/journal.pone.0135139

[…] wells., this chemical analytical method first comprised clustering of the 56 drug-like hits prioritized from the hts into 39 clusters by using the complete linkage algorithm implemented in the scaffold hunter program []. these clusters were complemented with all the analogs in tcams showing a tanimoto similarity ≥ 0.8 to any of the 56 prioritized compounds (molecules were represented […]


Clustered Distribution of Natural Product Leads of Drugs in the Chemical Space as Influenced by the Privileged Target Sites

Sci Rep
PMCID: 5380136
PMID: 25790752
DOI: 10.1038/srep09325

[…] own software, which can distinguish different molecules non-distinguishable by the 881-bit pubchem molecular fingerprints., in deriving the molecular scaffold trees of the 442 nplds and 137,836 nps, scaffold hunter v2.3.0 was used to select the nplds and nps with ring structures and to subsequently cluster them into molecular scaffold trees by using default rule set in the scaffold tree […]


Global Analysis Reveals Families of Chemical Motifs Enriched for hERG Inhibitors

PLoS One
PMCID: 4336329
PMID: 25700001
DOI: 10.1371/journal.pone.0118324

[…] an edge to two ‘child’ scaffolds in this network, where each ‘child’ is generated by removing one of the core rings from the parent. the scaffold network was computed using the java source code for scaffold hunter [], modified to implement an exhaustive enumeration of all possible inter-scaffold connections []., lastly, we computed a three-dimensional similarity network based […]


Identification of Small Molecule Frequent Hitters from AlphaScreen High Throughput Screens

J Biomol Screen
PMCID: 4153540
PMID: 24371213
DOI: 10.1177/1087057113516861

[…] scaffolds and comparative analysis of substituents in the scaffold nodes for active and inactive compounds as well as grouping chemicals based on structural similarity and proposed mode of action. scaffold hunter, isida, and silicos-it scaffolds were analyzed using the setcompare utility of the online chemical modeling environment (ochem) platform, and overrepresented structural elements […]

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Scaffold Hunter institution(s)
Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany; Chemical Biology, Technical University of Dortmund, Dortmund, Germany; Chair of Algorithm Engineering, Department of Computer Science, Technical University Dortmund, Dortmund, Germany; Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany; University of New Mexico School of Medicine, Division of Biocomputing, University of New Mexico, Albuquerque, New Mexico, USA
Scaffold Hunter funding source(s)
This work was supported by the Max Planck Society, the State of North-Rhine Westphalia, the European Union Fonds for Regional Development, the German Federal Ministry for Education and Research through the German National Genome Research Network-Plus (NGFN-Plus, grant number BMBF 01GS08102) and the US National Institutes of Health grant 1U54MH084690.

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