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PaDEL-descriptor specifications

Information


Unique identifier OMICS_18215
Name PaDEL-descriptor
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A single structural file or a directory containing the molecules' structural files.
Input format MDL mol, SMILES
Output data A complete descriptor.
Output format CSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.21
Stability Stable
Source code URL http://www.yapcwsoft.com/dd/padeldescriptor/PaDEL-Descriptor_src.zip
Maintained Yes

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  • person_outline Chun Wei Yap <>

Publication for PaDEL-descriptor

PaDEL-descriptor in pipeline

2018
PMCID: 5826228
PMID: 29515993
DOI: 10.3389/fchem.2018.00030

[…] from chemical structures, physicochemical or topological properties. currently thousands of continuous and discrete molecular descriptors can be obtained via chemoinformatics toolkits such as padel-descriptor (yap, ), openbabel (o'boyle et al., ), cdkit (steinbeck et al., ), rdkit (landrum, ), or web servers like e-dragon (tetko et al., ), chembcpp (dong et al., ), and chemdes (dong et […]

PaDEL-descriptor in publications

 (27)
PMCID: 5862716
PMID: 29564572
DOI: 10.1186/s13065-018-0401-x

[…] criterion of 0.01 kcal/mol å. to describe the compound structural diversity and in order to obtain validated qsar models. the optimized structures were saved in sdf format, and transferred to padel-descriptor version 2.18 tool kits, topological descriptors encode the chemical properties have been calculated for each aminooxadiazole, using padel server []. only three suitable ones […]

PMCID: 5872495
PMID: 29589559
DOI: 10.1186/s12859-018-2060-2

[…] line encyclopedia https://portals.broadinstitute.org/ccle., drug target data and structure files are taken from pubchem https://pubchem.ncbi.nlm.nih.gov/. chemical descriptors are generated using padel-descriptor software http://www.yapcwsoft.com/dd/padeldescriptor/ using the structure files. gene expression and area under the curve values for cell lines is available in the genomics of drug […]

PMCID: 5826228
PMID: 29515993
DOI: 10.3389/fchem.2018.00030

[…] from chemical structures, physicochemical or topological properties. currently thousands of continuous and discrete molecular descriptors can be obtained via chemoinformatics toolkits such as padel-descriptor (yap, ), openbabel (o'boyle et al., ), cdkit (steinbeck et al., ), rdkit (landrum, ), or web servers like e-dragon (tetko et al., ), chembcpp (dong et al., ), and chemdes (dong et […]

PMCID: 5835004
PMID: 29516034
DOI: 10.1016/j.dib.2018.01.077

[…] names., these structures were curated using chemaxon standardizer to remove salts and solvents and aromatized., the cfssubseteval algorithm selected subsets of structural descriptors (generated by padel descriptor ) for each dataset., the applicability domain of each dataset compared to the pharm dataset was quantified using leverage, euclidean distance from centroid, and a variable knn-based […]

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

[…] descriptor model highlighted descriptors recognized to be important in driving chemical distribution and uptake including bioconcentration factor (bcf) and bioavailability (bio). additionally, the padel descriptor set added autocorrelation metrics (atsc4m and aatsc1m) and logp (alogp). the toxprint descriptor set was generally less important but did reflect that organophosphate structures […]

PaDEL-descriptor institution(s)
Department of Pharmacy, Pharmaceutical Data Exploration Laboratory, National University of Singapore, Singapore
PaDEL-descriptor funding source(s)
This work was supported by the National University of Singapore (NUS) start-up grant R-148-000-105-133.

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