Virtual Protein Universe
Navigate the theoretical space of protein sequences. Separate what can be calculated, what databases report, and what still requires experiments.
About this project
Description. Virtual Protein Universe is an interactive, browser-based workbench for exploring protein sequences. Inspired by the Library of Babel, it starts from the idea that the number of possible amino-acid sequences is astronomically larger than anything nature has produced, and it lets you measure that space, analyse individual sequences, look up known proteins, compare variants and view predicted structures.
Aim.
- Make the scale of protein sequence space tangible and teach basic sequence properties (molecular weight, pI, hydropathy).
- Keep four kinds of information visibly separate: what is calculated here, what a database reports, what a model predicts, and what has been shown by experiment.
- Provide a credible foundation for responsible protein-exploration tools, where every feature states what it can and cannot show.
What this is not: it is not a discovery engine, not a diagnostic tool, and nothing here is experimental evidence. A valid sequence is not proof that a protein folds, works or is safe. Educational and exploratory use only; not for diagnosis, treatment or clinical decisions.
1. Sequence Space Calculator
Possible sequences of exactly N residues using the 20 standard amino acids (20N)
1.27 × 10130
This is the theoretical sequence count, not the number of proteins known to exist or fold. It counts only sequences of length exactly N, and it counts every distinct string, including the overwhelming majority that would never fold or function.
2. Sequence Analyzer
Calculated properties
Length (residues)
Molecular weight (average)
Theoretical pI
Average hydropathy (GRAVY)
Amino-acid composition
- Molecular weight: sum of average residue masses plus one water (18.015 Da), i.e. the unmodified, neutral polypeptide. Not a measured mass; excludes the initiator-Met removal, signal peptides, disulfides, glycans and other modifications.
- Theoretical pI: pH at which the net charge is zero, using the EMBOSS pK set, free N- and C-termini and no local-environment effects. Other published pK sets shift the result by several tenths of a pH unit, so treat it as an estimate, not a measurement.
- GRAVY: arithmetic mean of Kyte-Doolittle hydropathy values over all residues (positive = more hydrophobic overall).
3D structure prediction (optional)
Clicking this sends the analyzed sequence to a third-party server (the public ESM Atlas service, api.esmatlas.com). Do not use it for confidential sequences. Works for 16 to 400 residues. The result is a computational prediction, not experimental evidence, and random or designed sequences often give low-confidence, unstructured models.
3. UniProt Database Search
Search known protein records by protein name, gene, organism, or function keywords. This is a text/database search, not a sequence-similarity search.
4. Mutation Comparison
For equal-length sequences, compare residues position by position. "Compare" reports substitutions only and needs equal lengths. "Align" runs a global pairwise alignment (Needleman-Wunsch, simple scoring: match +2, mismatch -1, gap -2, up to 2,000 residues each) and reports substitutions, insertions and deletions. Positions are counted from the first residue you enter (so an initiator Met counts as position 1).
5. Evidence and Validation
The cards below report evidence actually available in this prototype. A valid amino-acid string is not proof that a protein folds, works, or is medically useful.
Level 1: Sequence syntax
No sequence analyzed.
Level 2: Structural plausibility
No structure-prediction model is connected. Structural plausibility is not assessed.
Level 3: Experimental function
No laboratory assay data are collected by this tool. Function is not experimentally verified.
Level 4: Medical utility
No clinical safety, efficacy, pharmacokinetic, or regulatory assessment is performed.
Roadmap (planned, not yet available)
These need a server and are not part of this page. They are listed so nothing is mistaken for an existing feature.
- Similarity search (BLAST) to show how close a sequence is to known proteins.
- Structure prediction for new sequences, with confidence scores, labelled as predictions.
- Protein language-model scoring of every single mutation of a sequence.
- Curated disease and variant annotations next to each UniProt record.
- Recording of real laboratory results, which is what Level 3 of the evidence panel requires.