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

Open access
Yap, Chun Wei·2011·Journal of Computational Chemistry
DOI 10.1002/jcc.21707
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Abstract

Introduction: 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. Methods: PaDEL‐Descriptor was developed using the Java language and consists of a library component and an interface component. The library component allows it to be easily integrated into quantitative structure activity relationship software to provide the descriptor calculation feature while the interface component allows it to be used as a standalone software. The software uses a Master/Worker pattern to take advantage of the multiple CPU cores that are present in most modern computers to speed up calculations of molecular descriptors. Results: The software has several advantages over existing standalone molecular descriptor calculation software. It is free and open source, has both graphical user interface and command line interfaces, can work on all major platforms (Windows, Linux, MacOS), supports more than 90 different molecular file formats, and is multithreaded. Conclusion: PaDEL‐Descriptor is a useful addition to the currently available molecular descriptor calculation software. The software can be downloaded at http://padel.nus.edu.sg/software/padeldescriptor. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

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Metadata

Authors
Yap, C. W.
Venue
Journal of Computational Chemistry
Publisher
Wiley
Published
2010-12-17
Volume
32
Issue
7
Pages
1466-1474
ISSN
  • 0192-8651 (ISSN-L)
  • 1096-987X
DOI
10.1002/jcc.21707
OpenAlex
W2159887157
Cited by
2,962
References
2
FWCI
26.55
Type
journal article
Language
en
Open access
hybrid
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)

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