Open-source

Open source tools are fundamental to advancing drug discovery. In this section you can find tools available for use in academia and industry.

In the case that any of the open-source tools have been useful for your research, we will appreciate if you cite Pharmacelera in your published material:

J. Vázquez, A. Deplano, A. Herrero, E. Herrero, open source section of Pharmacelera (https://pharmacelera.com/open-source/)

Conformer Generation Script (Python 3.0)

Open-source python script that allows generating conformations with RDKit, one of the best free tools available for conformer generation, due to its accuracy reproducing experimentally determined structures, and its modest computing requirements.

Jupyter Notebook for library analysis

Pharmacelera has developed a Jupyter Notebook to help with the analysis of the vHTS results. This Python 3.0 tool uses the RDKit chemical toolbox to calculate different molecular parameters.

Conformer Generation Script (Python 3.0)

Open-source python script that allows generating conformations with RDKit, one of the best free tools available for conformer generation, due to its accuracy reproducing experimentally determined structures, and its modest computing requirements.

Jupyter Notebook for library analysis

Pharmacelera has developed a Jupyter Notebook to help with the analysis of the vHTS results. This Python 3.0 tool uses the RDKit chemical toolbox to calculate different molecular parameters.

RDKit conformation generation script (Python 3)

At Pharmacelera we have written a python script to generate conformations with RDKit,
one of the best freely available tools for conformer generation due to
its accuracy reproducing experimentally determined structures and its
reasonable computing requirements. You can learn more about this script here.

New features from the previous version are:

  • Calculation of conformer energy and difference with minimum energy one.
  • Better control about what is happening if a molecule fails.
  • Possibility to generate a log file to check the different steps done
  • If MMFF does not work, automatic calculation with UFF (and warning of the molecule).
  • Better control of stereochemistry configuration according to the input molecule.
DOgQgBHWAAADR7V

Jupyter Notebook for library analysis

Pharmacelera has developed a Jupyter Notebook to help with the analysis of the vHTS results. This Python 3.0 tool uses the RDKit chemical toolbox to calculate different molecular parameters. The information generated is represented in the form of interactive graphs that the user can explore to make better decisions in choosing molecules with better properties.

Read more about Notebook.

radial

Contact

CONTACT INFORMATION

HEADQUARTERS

Torre R, 4a planta, Despatx A05, Parc Científic de Barcelona (PCB). C/ Baldiri Reixac 4-8 08028 Barcelona

ITALY S-IN Soluzioni Informatiche

Contact: Luca Sartori
Via G. Ferrari 14, 36100 Vicenza - Italy