Modules and Open-Source

Scientific Workflow Systems modules and open source software developed by pharmacelera

Modules & Nodes

Scientific Workflow Systems (SWS) facilitate the automatization of data analysis using different tools (modules) developed by third parties. These workflow platforms allow the combination of different software modules, where the output of one module is connected to the input of the next module, creating complex workflows intuitively. At Pharmacelera, we develop modules based on our technology that are incorporated directly into the most important cheminformatics SWS.

All the listed modules can be downloaded and installed directly from the listed SWS. However, in order to use them, a license is required. Please, contact our team and ask for the corresponding module license.

If your preferred SWS is not listed and you are still interested in a particular module, let us know and we will contact you soon.

Ligand preparation node (KNIME)
Module for small molecule library preparation. Includes the generation of compound conformers and hydrophobic fields calculations using our unique and superior molecular descriptors. Several input file formats are accepted.
Virtual Screening node (KNIME)
Module for ligand-based virtual screening of your compound libraries using our unique and superior molecular descriptors and 3D field-based molecular comparisons.
Docking Rescoring node (KNIME)
Module that improves the scoring function of molecular docking for structure-based virtual screening using our unique and superior molecular descriptors. Currently available to enhance the results of Glide, Gold and rDock molecular docking tools.


We also develop open-source code and make it available for scientists in academia and industry. You can download the tools directly to your local drive and use them. 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, E. Herrero, open source section of Pharmacelera (

Conformer generation script
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. Learn more.
ROC curve generation script
Open-source python script for the generation of ROC curves.