Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening.

ABSTRACT: Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing e

SUBMITTER: Ropp PJ 

PROVIDER: S-EPMC6534830 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature