PRIME viral mutation-space evaluation
Evaluation framework for protein representations on SARS-CoV-2 receptor-binding-domain mutants: ACE2 binding and expression regression under a random split and a position-stratified split that holds out mutated positions.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results on linked records
This benchmark has no results of its own in this release. 8 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, R² Protocol · part of this benchmark · 21 evaluations · 21 results
- PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, RMSE Protocol · part of this benchmark · 21 evaluations · 21 results
- PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, R² Protocol · part of this benchmark · 21 evaluations · 21 results
- PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, RMSE Protocol · part of this benchmark · 21 evaluations · 21 results
- PRIME ACE2 binding regression, Random split over RBD mutants, R² Protocol · part of this benchmark · 21 evaluations · 21 results
- PRIME ACE2 binding regression, Random split over RBD mutants, RMSE Protocol · part of this benchmark · 21 evaluations · 21 results
- PRIME RBD expression regression, Random split over RBD mutants, R² Protocol · part of this benchmark · 21 evaluations · 21 results
- PRIME RBD expression regression, Random split over RBD mutants, RMSE Protocol · part of this benchmark · 21 evaluations · 21 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 16 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, R² · 0/2 roles measured
- PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, RMSE · 0/2 roles measured
- PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, R² · 0/2 roles measured
- PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, RMSE · 0/2 roles measured
- PRIME ACE2 binding regression, Random split over RBD mutants, R² · 0/2 roles measured
- PRIME ACE2 binding regression, Random split over RBD mutants, RMSE · 0/2 roles measured
- PRIME RBD expression regression, Random split over RBD mutants, R² · 0/2 roles measured
- PRIME RBD expression regression, Random split over RBD mutants, RMSE · 0/2 roles measured
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Original source · Version of record, BMC Genomics 2026 (PMC13425921 JATS full text)
Technical metadata and extraction receipts
Stable ID: lit-protein-20261011-prime-benchmark-prime
- areas
- protein-function
- contexts
- research
- entity level
- suite
- version
- As published 2026
- task
- Predict RBD mutant binding and expression from protein language model representations
- scope note
- The position-stratified split holds out whole mutated positions, so it measures generalisation to unseen positions rather than unseen mutants.
- source locator
- Table 1 and its surrounding Results text
- limitations
- One protein (SARS-CoV-2 RBD) and two phenotypes; results do not transfer to other proteins without further evidence.; Author-reported: the PRIME authors ran every model and also contribute the fine-tuned ESM-RBD variants, which are the best-scoring rows.
Related records
- part of: PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, R²
- part of: PRIME ACE2 binding regression, Position-stratified split holding out whole mutated positions, RMSE
- part of: PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, R²
- part of: PRIME RBD expression regression, Position-stratified split holding out whole mutated positions, RMSE
- part of: PRIME ACE2 binding regression, Random split over RBD mutants, R²
- part of: PRIME ACE2 binding regression, Random split over RBD mutants, RMSE
- part of: PRIME RBD expression regression, Random split over RBD mutants, R²
- part of: PRIME RBD expression regression, Random split over RBD mutants, RMSE