Detection and Visualization of Protein Interactions with Protein Fragment Complementation Assays
Bibliographic record
Abstract
A first step in defining the function of a novel gene is to determine its interactions with other gene products in an appropriate context; that is, because proteins make specific interactions with other proteins as part of functional assemblies, an appropriate way to examine the function of the product of a novel gene is to determine its physical relationships with the products of other genes. This is the basis of the highly successful yeast two-hybrid system (1–6). The central problem with two-hybrid screening is that detection of protein-protein interactions occurs in a fixed context, the nucleus of S. cerevisiae, and the results of a screening must be validated as biologically relevant using other assays in appropriate cell, tissue or organism models. While this would be true for any screening strategy, it would be advantageous if one could combine library screening with tests for biological relevance into a single strategy, thus tentatively validating a detected protein as biologically relevant and eliminating false-positive interactions immediately. It was with these challenges in mind that our laboratory developed the protein-fragment complementation assay (PCA) strategy. In this strategy, the gene for an enzyme is rationally dissected into two pieces. Fusion proteins are constructed with two proteins that are thought to bind to each other, fused to either of the two probe fragments. Folding of the probe protein from its fragments is catalyzed by the binding of the test proteins to each other and is detected as reconstitution of enzyme activity.
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 distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".