Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions
… compared, themes identified, and gaps noted, and suggestions recommended … prediction
results of known scoring functions allowing a fair comparison of the model with existing scoring …
results of known scoring functions allowing a fair comparison of the model with existing scoring …
Featurization strategies for protein–ligand interactions and their applications in scoring function development
… The authors attributed the success of NNScore to its integration strategy in feature extraction…
), the energy difference between those orbitals (E GAP ), electronegativity (χ), and so on. The …
), the energy difference between those orbitals (E GAP ), electronegativity (χ), and so on. The …
[HTML][HTML] Scoring functions for protein-ligand binding affinity prediction using structure-based deep learning: a review
… The success of supervised machine learning and deep … In this way, protein-ligand interactions
are encoded implicitly … The authors highlight a significant performance gap between in-…
are encoded implicitly … The authors highlight a significant performance gap between in-…
Protein–protein docking: Past, present, and future
S Sunny, PB Jayaraj - The protein journal, 2022 - Springer
… a considerable gap between the number of individual protein … This addition made a drastic
increase in the success rate of … the scoring phase precisely determine the quality of predictions…
increase in the success rate of … the scoring phase precisely determine the quality of predictions…
Machine learning and ligand binding predictions: a review of data, methods, and obstacles
SR Ellingson, B Davis, J Allen - … et Biophysica Acta (BBA)-General Subjects, 2020 - Elsevier
… The ability to accurately predict protein-ligand interactions … The success of these models is
typically measured in dataset … This gap gets smaller with aofb, but still exists. Strangely, the …
typically measured in dataset … This gap gets smaller with aofb, but still exists. Strangely, the …
Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term
… redocking and cross-docking success rates, indicating that it … and distance gap between
shells (14 shells and distance gap of … He is working on protein-ligand interaction prediction and …
shells (14 shells and distance gap of … He is working on protein-ligand interaction prediction and …
Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction
… used to characterize the protein–ligand complex in an ML-… , RF-score, with the application of
RF to predict protein–ligand binding … We calculated the MM-GBSA residue-ligand interaction …
RF to predict protein–ligand binding … We calculated the MM-GBSA residue-ligand interaction …
A new paradigm for applying deep learning to protein–ligand interaction prediction
… structures predicted by AlphaFold2, the overall top 1 success … began to directly predict the
RMSD of docking poses (such … [38]), or use scores from other mathematical spaces (such as …
RMSD of docking poses (such … [38]), or use scores from other mathematical spaces (such as …
Scoring of protein–protein docking models utilizing predicted interface residues
G Pozzati, P Kundrotas… - Proteins: Structure …, 2022 - Wiley Online Library
… in the docking success when applying interface predictions to the scoring of the docking
poses. … A large performance gap can be observed with different contact prediction methods. …
poses. … A large performance gap can be observed with different contact prediction methods. …
[HTML][HTML] Ssnet: A deep learning approach for protein-ligand interaction prediction
… based [5] PLI predictions, have been developed, with limited success. Often, these methods
… of docking scores obtained from each docking method. For each target, the docking scores …
… of docking scores obtained from each docking method. For each target, the docking scores …