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Protocols

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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Maintainer


  • person_outline Chun Wei Yap

Publication for PaDEL-descriptor

PaDEL-descriptor citations

 (35)
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QSAR study and rustic ligand based virtual screening in a search for aminooxadiazole derivatives as PIM1 inhibitors

2018
Chem Cent J
PMCID: 5862716
PMID: 29564572
DOI: 10.1186/s13065-018-0401-x
call_split See protocol

[…] ergence 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 have been […]

library_books

Investigation of model stacking for drug sensitivity prediction

2018
BMC Bioinformatics
PMCID: 5872495
PMID: 29589559
DOI: 10.1186/s12859-018-2060-2

[…] Cell 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 Se […]

library_books

In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts

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

[…] culated 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 al. […]

library_books

Mordred: a molecular descriptor calculator

2018
J Cheminform
PMCID: 5801138
PMID: 29411163
DOI: 10.1186/s13321-018-0258-y

[…] ties of the compounds in the test dataset that are not used for model construction.Although both open-source and proprietary software have been developed for calculating molecular descriptors—such as PaDEL-Descriptor [], BlueDesc [], ChemoPy [], PyDPI [], Rcpi [], cinfony [], and Dragon []—they each have advantages and disadvantages (Table ). The freely available PaDEL-Descriptor can calculate 187 […]

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QSAR ligand dataset for modelling mutagenicity, genotoxicity, and rodent carcinogenicity

2018
PMCID: 5835004
PMID: 29516034
DOI: 10.1016/j.dib.2018.01.077
call_split See protocol

[…] The CfsSubsetEval algorithm selected subsets of structural descriptors (generated by PaDEL Descriptor ) for each dataset. […]

call_split

Network pharmacological mechanisms of Vernonia anthelmintica (L.) in the treatment of vitiligo: Isorhamnetin induction of melanogenesis via up regulation of melanin biosynthetic genes

2017
BMC Syst Biol
PMCID: 5691595
PMID: 29145845
DOI: 10.1186/s12918-017-0486-1
call_split See protocol

[…] tic prediction of compound-target interactions, particularly new chemical entities []. For this purpose, the canonical SMILES format was converted into the substructure fingerprint (FP4) format using PaDEL-Descriptor software (version 2.18) []. For each compound, the top 20 predicted targets were stored as putative targets. The targets were subsequently normalized to the official gene name using t […]


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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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