How to use ProTrek Online

Use ProTrek online for sequence, structure, and text retrieval across Swiss-Prot.

ProTrek embeds protein sequences, structures, and biological descriptions into a shared space. Choose a Query Type and Search Target, then provide the corresponding input. Neurosnap uses ProTrek 650M and the complete published Swiss-Prot index collection; this is a fixed database snapshot, not a live UniProt search.

How ProTrek Works

Sequence queries accept one protein of 10–1022 residues. Structure queries accept one chain and model, converted into Foldseek 3Di tokens. Text queries accept up to 4000 characters and 510 word pieces; inputs are never silently truncated. Each job embeds its query and searches the selected precomputed index locally.

Proteins returns accessions and amino acid sequences. Structures returns accessions and 3Di structural sequences, not downloaded coordinates or structural alignments. Annotations returns the retrieved text from one of all 56 published categories, including Global, Function, catalytic information, and residue annotations. A residue annotation match does not identify a position in the query protein.

results.csv contains up to Maximum Hits ranked by Matching Score: the normalized embedding inner product divided by the model's learned temperature. Scores are retrieval similarities, not probabilities, sequence identities, TM-scores, or experimentally validated function assignments. Compare scores within a search; categories and modalities have different score distributions. Very close displayed scores may differ before rounding. Annotation matches do not necessarily identify a unique protein.

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 ProTrek on Neurosnap

Using ProTrek on Neurosnap could drastically accelerate cross-modal protein discovery and annotation retrieval.

Find candidate proteins from a functional description.
Retrieve related proteins from sequence or structural queries.
Explore all published Swiss-Prot annotation categories with ranked, downloadable results.

How to Use ProTrek on Neurosnap

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

A trimodal protein language model enables advanced protein searches. Nature Biotechnology (2025). doi:10.1038/s41587-025-02836-0.

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

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