ProtaBank: A repository for protein design and engineering data
Bibliographic record
Abstract
Abstract We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org . Impact The ProtaBank database provides a central repository for researchers to store, query, analyze, and share all types of protein engineering data. This modern database will serve a pivotal role in organizing protein engineering data and leveraging the increasingly large amounts of mutational data being generated. Together with the analysis tools, it will help scientists gain insights into sequence-function relationships, support the development of new predictive tools and algorithms, and facilitate future protein engineering efforts. Abbreviations 3D three-dimensional API application programming interface AWS Amazon Web Services BLAST Basic Local Alignment Search Tool C m concentration of denaturant at midpoint of unfolding transition CSV comma-separated values Δ G Gibbs free energy of folding/unfolding Gβ1 β1 domain of Streptococcal protein G GdmCl guanidinium chloride k cat catalytic rate constant K d dissociation constant MIC minimum inhibitory concentration PDB Protein Data Bank PE protein engineering RDS Relational Database Services REST Representation State Transfer T m melting temperature
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.008 | 0.027 |
| Meta-epidemiology (narrow) | 0.003 | 0.002 |
| Meta-epidemiology (broad) | 0.004 | 0.003 |
| Bibliometrics | 0.009 | 0.014 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.011 | 0.011 |
| Open science | 0.011 | 0.011 |
| Research integrity | 0.003 | 0.006 |
| Insufficient payload (model declined to judge) | 0.042 | 0.074 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".