How to use Pepsickle Proteasomal Cleavage Prediction Online

Use Pepsickle online to predict proteasomal cleavage sites from sequence context.

Pepsickle is a context-aware proteasomal cleavage predictor. Its default epitope-based model was trained on in-vivo epitope data and does not distinguish proteasome types. In-vitro gradient-boosted and experimental neural models support constitutive proteasome and immunoproteasome predictions.

Use it to investigate antigen processing and compare cleavage patterns across protein or peptide variants. Cleavage predictions alone do not establish antigen presentation, MHC binding, or immunogenicity.

How Pepsickle Proteasomal Cleavage Prediction Works

Submit Input Sequences and select Model. For either in-vitro model, choose Proteasome Type. Training Data selects standard all-mammal weights or experimental human-only weights. Cleavage Threshold defaults to 0.5.

Pepsickle uses eight residues on each side of the scored residue for epitope prediction, and three on each side for in-vitro prediction. Include surrounding sequence for sites of interest. Missing context at sequence ends is automatically padded with *; X represents an existing residue of unknown identity.

The prediction CSV uses one-based positions. Each score describes cleavage after the indicated residue. The final residue is set to zero and is never an internal cleavage site. Calls use unrounded probabilities strictly greater than the threshold; the exported values are rounded to three decimals. The summary excludes the final residue from mean and maximum probabilities. These are model estimates for experimental prioritization, not guarantees of cleavage.

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 Pepsickle Proteasomal Cleavage Prediction on Neurosnap

Using Pepsickle Proteasomal Cleavage Prediction on Neurosnap could drastically accelerate context-aware proteasomal cleavage screening for antigen-processing studies.

Screen multiple protein or peptide sequences in one submission.
Compare constitutive and immunoproteasomal digestion models.
Review probabilities, sequence context, and cleavage calls in downloadable CSVs.

How to Use Pepsickle Proteasomal Cleavage Prediction on Neurosnap

To harness the capabilities of Pepsickle Proteasomal Cleavage Prediction, 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 Pepsickle Proteasomal Cleavage Prediction.
Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
Run Tool: Submit the Pepsickle Proteasomal Cleavage Prediction 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 Pepsickle Proteasomal Cleavage Prediction in publications or research outputs.

Pepsickle: a tool for proteasomal cleavage prediction. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab628.

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

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