Featurization strategies for protein–ligand interactions and their applications in scoring function development
Bibliographic record
Abstract
Abstract The predictive performance of classical scoring functions (SFs) seems to have reached a plateau. Currently, SFs relying on sophisticated machine learning techniques have shown great potential in binding affinity prediction and virtual screening. As one of the most indispensable components in the workflow of training a machine learning scoring function (MLSF), the featurization or representation process enables us to catch certain physical processes that are important for protein–ligand interactions and to obtain machine‐readable descriptors. Currently, according to how they are derived, the descriptors used in MLSFs for both continuous and binary binding affinity estimates can be grouped into two broad categories: handcrafted features and automated‐extraction features. Moreover, the automated‐extraction features emerge as a new featurization trend along with the application of deep learning algorithms. Here, we make a thorough summary of the advances in the featurization strategies for protein–ligand interactions in the context of MLSFs, with emphasis on the recently rising automated‐extraction features. We also discuss the similarity between protein–ligand interaction representations and small‐molecule representations, and the challenges confronted by the scientific community in characterizing protein–ligand interactions. We expect that this review could inspire the development of novel featurization approaches and boosted MLSFs. This article is categorized under: Data Science > Artificial Intelligence/Machine Learning Software > Molecular Modeling Molecular and Statistical Mechanics > Molecular Interactions
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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 | 0.003 | 0.005 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| 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 | 0.002 |
| Insufficient payload (model declined to judge) | 0.003 | 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".