PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints

By Chun Wei Yap. 2011

2,633 citations recorded by the source corpus.

PaDEL‐Descriptor is a software for calculating molecular descriptors and fingerprints. The software currently calculates 797 descriptors (663 1D, 2D descriptors, and 134 3D descriptors) and 10 types of fingerprints. These descriptors and fingerprints are calculated mainly using The Chemistry Development Kit. Some additional descriptors and fingerprints were added, which include atom type electrotopological state descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth.

Subfields: Computational Theory and Mathematics, Physical and Theoretical Chemistry, Safety Research

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Citations in the corpus

Mordred: a molecular descriptor calculator (2018, methodology): “Although both open-source and proprietary software have been developed for calculating molecular descriptors—such as PaDEL-Descriptor [6], BlueDesc [7], ChemoPy [8], PyDPI [9], Rcpi [10], cinfony [11], and Dragon [12]—they each have advantages and disadvantages Open Access”
Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics (2018, methodology): “Retention times can be predicted by using chemical descriptors as input parameters which can be computed directly from structures by tools such as Dragon [115], MOLD2 [116] or PaDel [117].”
ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation (2015, methodology): “Existing tools for molecular descriptor and fingerprint calculation include DRAGON [27], BlueDesc [28], CDK Descriptor Calculator [29], PaDEL [30], Mold2 [31], ChemAxon JChem [32], ADMEWORKS Model-Builder [33], CDK [34], RDKit [35], Chemopy [36], etc.”
Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties (2012, methodology): “sg/software/ padeldescriptor/) [19] from the SMILES with default settings.”
OPERA models for predicting physicochemical properties and environmental fate endpoints (2018, methodology): “The curated chemical structures were used to calculate molecular descriptors using the free and open-source software PaDEL [96].”