How to Use MolGpKa

Commercially Available Online Web Server

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Formulation & Stability Ligand/Drug Design & Screening Formulation Ionization Property Prediction Small Molecules

Use MolGpKa online for site-level molecular pKa prediction.

Predict site-level acidic and basic pKa values with the pretrained MolGpKa graph-convolutional models. The service standardizes neutralizable molecules and reports the ionizable heavy atom using explicit atom-map numbers. Basic-site predictions require benchmark review before release; local upstream inference produced implausible results for some simple amines. Predictions do not include pH-dependent populations or macroscopic titration curves.

How MolGpKa Works

Submit Input Molecules as SMILES, CCD codes, or molecular structures. MolGpKa standardizes a neutral parent and predicts the sites recognized by its SMARTS rules. Permanently charged or disconnected entries are rejected.

results.csv lists site type, predicted pKa, and Heavy Atom Map Number. This number matches Standardized Mapped SMILES and does not refer to uploaded atom numbering. Acidic hydrogen sites are reported on the bonded heavy atom. summary.csv includes every molecule, including those with no recognized sites; missing sites do not imply a molecule cannot ionize.

The upstream code, rules, and bundled checkpoints are taken from one pinned MIT-licensed repository revision. No training dataset is redistributed. Local upstream inference returned approximately 2.06 for ethylamine and 1.70 for triethylamine, so this beta integration requires scientific benchmark review before release. Model predictions are screening estimates; use Dimorphite-DL separately for candidate protonation-state enumeration.

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 MolGpKa on Neurosnap

Using MolGpKa on Neurosnap could drastically accelerate Site-level molecular pKa prediction.

  • Acidic and basic site predictions using the upstream checkpoints.
  • Mapped SMILES identify the heavy atom associated with each predicted pKa.
  • Explicit reporting of molecules without recognized ionization sites.

How to Use MolGpKa on Neurosnap

To harness the capabilities of MolGpKa, researchers can follow this streamlined workflow within Neurosnap:

  1. Access Neurosnap: Start by logging in to the Neurosnap website.
  2. Select Tool: From the list of available tools, choose MolGpKa.
  3. Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
  4. Run Tool: Submit the MolGpKa job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
  5. 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 MolGpKa in publications or research outputs.

https://doi.org/10.1021/acs.jcim.1c00075

Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/

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