Protein secondary structure assignment using <i>pc</i> ‐polyline and convolutional neural network
Bibliographic record
Abstract
Abstract Motivation The assignment of protein secondary structure elements (SSEs) underpins structural analysis and prediction. The backbone of a protein could be adequately represented using a pc ‐polyline that passes through the centers of its peptide planes. One salient feature of pc ‐polyline representation is that the secondary structure of a protein becomes recognizable in a matrix whose elements are the pairwise distances between two peptide plane centers. Thus, a pc ‐polyline could in turn be used to assign SSEs. Results Using convolutional neural network (CNN) here we confirm that a pc ‐polyline indeed contains enough information for it to be used for the accurate assignments of the six SSE types: α ‐helix, β ‐sheet, β ‐bulge, 3 10 ‐helix, turn and loop. The applications to three large data sets show that the assignments by our CNN‐based p2psse program agree very well with those by dssp , stride and quite well with those by five other programs. The analyses of their SSE assignments raise some general questions about the characterizations of protein secondary structure. In particular the analyses illustrate the difficulty with giving a quantitative and consistent definition for each of the six SSE types especially for 3 10 ‐helix, β ‐bulge, turn or loop in terms of either backbone H‐bond patterns, or backbone dihedral angles, or C α ‐polyline or pc ‐polyline. The difficulty suggests that the SSE space though being dominated by the regions for the six SSE types is to a certain degree continuous. Availability The program is available at https://github.com/wlincong/p2pSSE .
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".