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Published October 14, 2020 | Version v1.0.0
Software Open

Jacob-Spiegel/SMILESClickChem: 1.0.0

Creators

  • 1. University of Pittsburgh

Description

This is the initial release of SMILESClickChem (Version 1.0.0)

SMILESClickChem is a cheminformatic, Python program that reacts one parent ligand (SMILES string) following predefined reactions to create a child compound. SMILESClickChem uses the mutation algorithm from the program AutoGrow4.

SMILESClickChem accepts a list of SMILES (in .smi format) and will attempt to produce a user-defined number of unique children SMILES. SMILESClickChem also allows users to apply chemical property filters using GlauconiteFilter. Additionally, SMILESClickChem options the automated conversion of the children from 1/2D SMILES to 3D representations (PDB and 3D-SDF) using Gypsum-DL.

Files

Jacob-Spiegel/SMILESClickChem-v1.0.0.zip

Files (7.7 MB)

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Additional details

Related works

Is supplement to
https://github.com/Jacob-Spiegel/SMILESClickChem/tree/v1.0.0 (URL)

References

  • Spiegel, J.O., Durrant, J.D. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform 12, 25 (2020). https://doi.org/10.1186/s13321-020-00429-4
  • Spiegel, J.O., Targeting the poly (adp-ribose) polymerase-1 catalytic pocket using autogrow4, a genetic algorithm for de novo design (September 2020). URL http://d-scholarship.pitt.edu/39666/
  • Ropp, P.J., Spiegel, J.O., Walker, J.L. et al. Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. J Cheminform 11, 34 (2019). https://doi.org/10.1186/s13321-019-0358-3
  • Ropp, P.J., Kaminsky, J.C., Yablonski, S. et al. Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules. J Cheminform 11, 14 (2019). https://doi.org/10.1186/s13321-019-0336-9
  • Spiegel, J.O., Durrant, J.D., GlauconiteFilter: an open-source program for automated ADME-PK filtering. (2020) https://doi.org/10.5281/zenodo.4087648
  • Durrant JD, McCammon JA (2012) AutoClickChem: Click Chemistry in Silico. PLOS Computational Biology 8(3): e1002397. https://doi.org/10.1371/journal.pcbi.1002397
  • Markus Hartenfeller, Martin Eberle, Peter Meier, Cristina Nieto-Oberhuber, Karl-Heinz Altmann, Gisbert Schneider, Edgar Jacoby, and Steffen Renner Journal of Chemical Information and Modeling 2011 51 (12), 3093-3098 DOI: 10.1021/ci200379p