How to Use Dimorphite-DL
Commercially Available Online Web Server
Use Dimorphite-DL online for pH-dependent protonation state enumeration.
Enumerate candidate protonation states over a chosen pH interval using Dimorphite-DL ionization rules. Outputs retain each input molecule identity and show the state SMILES and formal charge. State enumeration does not provide pKa predictions or equilibrium populations.
How Dimorphite-DL Works
Supply Input Molecules and choose a Minimum pH and Maximum pH between 0 and 14. Equal endpoints enumerate at one pH. The uncertainty factor expands the rule-based pKa windows.
results.csv contains one row per candidate state with the input index and name. These states are candidates, not population estimates or individually predicted pKa values. Runs reaching the internal 128-state limit fail with guidance to narrow the pH range rather than silently returning an incomplete list. Dimorphite-DL and its bundled rules are Apache-2.0 licensed.
What is Neurosnap?
Neurosnap is the leading platform for bioinformatics and computational science focused on expanding access to powerful modeling and simulation tools. Because many state-of-the-art machine learning systems remain complex to install, configure, and scale, Neurosnap offers a clean, browser-based workspace that removes the burden of infrastructure management, dependency conflicts, and command-line tooling.
Built for biologists, chemists, and cross-disciplinary scientists, the platform enables advanced computational workflows without requiring expertise in software engineering or cloud architecture. Researchers can launch analyses through an intuitive interface, connect programmatically through a comprehensive API, and rely on automated resource management to scale workloads efficiently. By taking care of the underlying compute and operational complexity, Neurosnap allows teams to devote their energy to scientific progress and faster iteration. Security and data protection remain foundational principles, with clear safeguards outlined in our Terms of Use and Privacy Policy to ensure your work stays protected.
Advancing Discovery with Dimorphite-DL on Neurosnap
Using Dimorphite-DL on Neurosnap could drastically accelerate pH-dependent protonation state enumeration.
- Accepts SMILES, CCD, and molecular structure files.
- Returns candidate state SMILES and formal charges for a pH interval.
How to Use Dimorphite-DL on Neurosnap
To harness the capabilities of Dimorphite-DL, researchers can follow this streamlined workflow within Neurosnap:
- Access Neurosnap: Start by logging in to the Neurosnap website.
- Select Tool: From the list of available tools, choose Dimorphite-DL.
- Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
- Run Tool: Submit the Dimorphite-DL job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
- Review Output: Explore your results through rich visualizations, including figures, plots, and interactive views designed to help you analyze findings with clarity and confidence.
Citations
Please cite the original work when using Dimorphite-DL in publications or research outputs.
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https://doi.org/10.1186/s13321-019-0336-9 |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |
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