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molBLOCKS specifications


Unique identifier OMICS_23116
Name molBLOCKS
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 0.1
Stability Stable
Source code URL
Maintained Yes


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  • person_outline Mona Singh <>

Additional information

Publication for molBLOCKS

molBLOCKS in publications

PMCID: 5836963
PMID: 29063731
DOI: 10.1111/cbdd.13129

[…] the generation of small fragments that do not describe properly the fragment space associated to the deletion analogues. we present significant modifications to the molecular fragmentation programme molblocks, which allows the exhaustive sampling of the fragment space associated with a molecule to generate all possible molecular fragments. this generates larger fragments, by combining […]

PMCID: 5818596
PMID: 29075892
DOI: 10.1007/s00204-017-2067-x

[…] has undergone extensive curation using an automated knime workflow designed for the purpose of validating and correcting the chemical structures and their identifiers such as cas, names, smiles and molblocks (mansouri et al. ). the curated physprop datasets were then processed through a standardization workflow to generate the qsar-ready structures used for modeling (mansouri et al. ). […]

PMCID: 5608908
PMID: 28935948
DOI: 10.1038/s41598-017-12170-4

[…] on tanimoto index screening are available in supplementary figure ., starting from the chemical structures of the identified cruzipain inhibitors, several molecular fragments were obtained using molblocks (fig. ). all fragments were used as queries in substructure searches against the chembl database (release 22.1) to retrieve structurally related bioactive compounds. these compounds […]

PMCID: 4980782
PMID: 27510651
DOI: 10.1186/s12920-016-0205-6

[…] and natural products were directly obtained from the drugbank and supernatural ii databases, respectively., both drugs and natural products were fragmented with the fragment program, part of the molblocks suite [], which breaks molecules along chemically important bonds and returns the corresponding fragments (or putative building blocks). the list of chemical bonds that were used […]

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molBLOCKS institution(s)
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA
molBLOCKS funding source(s)
Supported by the American-Italian Cancer Foundation Postdoctoral Fellowship, NIH R01 GM076275 and NSF ABI 1062371.

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