ArticleJournal of cheminformatics2019
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening.
Article in Journal of cheminformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
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- An aerosolized dual-action autotaxin inhibitor-PPARγ agonist for the treatment of pulmonary fibrosis.Cell reports. Medicine · 2026Article
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- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- In silico assessment of neuromuscular blocking agents and fluoroquinolones as ligands of the Mas-related G protein-coupled receptor X2.Pharmacological reports : PR · 2026Article
- Using a Novel Consensus-Based Chemoinformatics Approach to Predict ADMET Properties and Druglikeness of Tyrosine Kinase Inhibitors.International journal of molecular sciences · 2025Review
- Ameliorative role of Polyscias fruticosa leaf extract in aluminum chloride-induced neurotoxicity flies possibly mediated by N-methyl-D-aspartate receptor antagonistic and anticholinesterase active compounds.Journal of natural medicines · 2025Article
- Pharmacological evaluation of physcion as a TRPV1 inhibitor with multimodal analgesic efficacy in experimental pain models.Biological research · 2025Article
- A gain-of-function mutation in ATP6V0A4 drives primary distal renal tubular alkalosis with enhanced V-ATPase activity.The Journal of clinical investigation · 2025Article
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- Identification and evaluation of a pinocembrin analog as a TRPV1 inhibitor with analgesic properties in murine pain models.Frontiers in pharmacology · 2025Article
- Accelerating Ligand Discovery for Insect Odorant Receptors.International journal of biological sciences · 2025Article
- Acidic sphingomyelinase interactions with lysosomal membranes and cation amphiphilic drugs: A molecular dynamics investigation.Computational and structural biotechnology journal · 2024Article
- The potential inhibitory mechanism of EGCG against the Chikungunya virus targeting non-structural protein 2 through molecular dynamics simulation.Scientific reports · 2024Article
- Reversible Control of Native GluN2B-Containing NMDA Receptors with Visible Light.ACS chemical neuroscience · 2024Article
- The changing scenario of drug discovery using AI to deep learning: Recent advancement, success stories, collaborations, and challenges.Molecular therapy. Nucleic acids · 2024Review
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Authors and funding
8 authors.
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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 each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0.
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