Fast and Flexible Protein Design Using Deep Graph Neural Networks
Bibliographic record
Abstract
Protein structure and function is determined by the arrangement of the linear sequence of amino acids in 3D space. We show that a deep graph neural network, ProteinSolver, can precisely design sequences that fold into a predetermined shape by phrasing this challenge as a constraint satisfaction problem (CSP), akin to Sudoku puzzles. We trained ProteinSolver on over 70,000,000 real protein sequences corresponding to over 80,000 structures. We show that our method rapidly designs new protein sequences and benchmark them in silico using energy-based scores, molecular dynamics, and structure prediction methods. As a proof-of-principle validation, we use ProteinSolver to generate sequences that match the structure of serum albumin, then synthesize the top-scoring design and validate it in vitro using circular dichroism. ProteinSolver is freely available at http://design.proteinsolver.org and https://gitlab.com/ostrokach/proteinsolver. A record of this paper's transparent peer review process is included in the Supplemental Information.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
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".