Gypsum-DL: A New Program that Prepares Molecular Libraries for Virtual Screening

Happy to announce that the Durrant Lab recently released Gypsum-DL, a program that prepares molecular libraries for virtual screening.

Structure-based virtual screening requires carefully prepared 3D models of potential small-molecule ligands. Existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. In contrast, Gypsum-DL is open source. It accepts virtual compound libraries in SMILES or flat SDF formats as input. For each molecule in the library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, it produces an SDF file with 3D coordinates assigned. A copy is available free of charge under the terms of the Apache License, Version 2.0:

Happy docking!

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. Patrick J. Ropp, Jacob O. Spiegel, Jennifer L. Walker, Harrison Green, Guillermo A. Morales, Katherine A. Milliken, John J. Ringe & Jacob D. Durrant. Journal of Cheminformatics. Volume 11, Article number: 34 (2019)

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.