Happy to announce that the Durrant Lab recently released Gypsum-DL, a program that prepares molecular libraries for virtual screening.
Excited to release Gypsum-DL, a program that prepares compound models (e.g., SMILES strings) for virtual screening. Aside from assigning 3D coordinates, it also considers alternate protonation, tautomeric, and ring conformational states. Learn more at https://t.co/zPuoHgdbAk
— DurrantLab (@LabDurrant) September 17, 2019
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: https://git.durrantlab.pitt.edu/jdurrant/gypsum_dl
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)