LGA-Dock/EM-Dock Exploring Lamarckian genetic algorithms and energy-based local search for ligandreceptor docking
Bibliographic record
Abstract
We report the development of LGA-Dock and EM-Dock, two SVL-based docking programs for flexible ligand rigid receptor docking applications. LGA-Dock is comprised of a stochastic population generator, a docking routine based on a Lamarckian genetic algorithm, and a local search function based on molecular mechanics (MM) energy minimization. Subsequent modifications of LGA-Dock to address performance issues produced EM-Dock, which proved to be as accurate and much faster than its predecessor despite the deletion of the genetic algorithm component. The basic performance of LGA-Dock and EM-Dock, compared with AutoDock and MOE™ 2004.03 docking routines is presented.Key words: docking, Lamarckian genetic algorithm, molecular mechanics, simulated annealing, tabu search, local search.
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 | 0.001 | 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".