ArticleJournal of cheminformatics2019
Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules.
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 53 papers.
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Who cites it
53 citing papers in PubMed.
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- A synergistic deep learning and machine learning framework for screening heterocyclic compounds against ALDH1A1.Molecular diversity · 2026Article
- PEP-EDIT: a web server for the 3D generation and interactive editing of complex peptides.Nucleic acids research · 2026Article
- CBR-db: A Cheminformatic Database for Biochemical Reaction Analysis.ACS synthetic biology · 2026Article
- In silico screening for safe and potent essential oils against mosquito neural targets.Frontiers in zoology · 2026Article
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- An aerosolized dual-action autotaxin inhibitor-PPARγ agonist for the treatment of pulmonary fibrosis.Cell reports. Medicine · 2026Article
- Benchmarking pJournal of chemical information and modeling · 2026Article
- Identification of ANT2 as a Druggable Target for Endocrine-Resistant ERα-Positive Breast Cancer.International journal of molecular sciences · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- DFDD: A Cloud-Ready Tool for Distance-Guided Fully Dynamic Docking in Host-Guest Complexation.Journal of chemical information and modeling · 2026Article
- PEAS: An Application for Autonomous Precision Conformation Sampling.Journal of chemical information and modeling · 2025Article
- MolAI: A Deep Learning Framework for Data-Driven Molecular Descriptor Generation and Advanced Drug Discovery Applications.Journal of chemical information and modeling · 2025Article
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- Ultrahigh-Throughput Virtual Screening Strategies against PPI Targets: A Case Study of STAT Inhibitors.Journal of chemical information and modeling · 2025Article
- State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor.Journal of chemical information and modeling · 2025Article
- Pharmacological evaluation of physcion as a TRPV1 inhibitor with multimodal analgesic efficacy in experimental pain models.Biological research · 2025Article
- PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures.Nucleic acids research · 2025Article
- Mitigating Molecular Aggregation in Drug Discovery With Predictive Insights From Explainable AI.Angewandte Chemie (International ed. in English) · 2025Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small-molecule protonation can promote or discourage protein binding by altering hydrogen-bond, electrostatic, and van-der-Waals interactions. To improve virtual-screen pose and affinity predictions, researchers must account for all major small-molecule ionization states. But existing programs for calculating these states have notable limitations such as high cost, restrictive licenses, slow execution times, and poor modularity. Here, we present dimorphite-DL 1.0, a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states. Dimorphite-DL uses a straightforward empirical algorithm that leverages substructure searching and draws on a database of experimentally characterized ionizable molecules. We have tested dimorphite-DL using several versions of Python and RDKit on all major operating systems. We release it under the terms of the Apache License, Version 2.0. A copy is available free of charge from http://durrantlab.com/dimorphite-dl/ .
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