Extended connectivity interaction features: improving binding affinity prediction through chemical description
Motivation Machine-learning scoring functions (SFs) have been found to outperform
standard SFs for binding affinity prediction of protein–ligand complexes. A plethora of …
standard SFs for binding affinity prediction of protein–ligand complexes. A plethora of …
Learning from the ligand: using ligand-based features to improve binding affinity prediction
Motivation Machine learning scoring functions for protein–ligand binding affinity prediction
have been found to consistently outperform classical scoring functions. Structure-based …
have been found to consistently outperform classical scoring functions. Structure-based …
[HTML][HTML] BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand …
HM Ashtawy, NR Mahapatra - BMC bioinformatics, 2015 - Springer
Background Accurately predicting the binding affinities of large sets of protein-ligand
complexes is a key challenge in computational biomolecular science, with applications in …
complexes is a key challenge in computational biomolecular science, with applications in …
Hac-net: A hybrid attention-based convolutional neural network for highly accurate protein–ligand binding affinity prediction
GW Kyro, RI Brent, VS Batista - Journal of Chemical Information …, 2023 - ACS Publications
Applying deep learning concepts from image detection and graph theory has greatly
advanced protein–ligand binding affinity prediction, a challenge with enormous ramifications …
advanced protein–ligand binding affinity prediction, a challenge with enormous ramifications …
SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes
D Zilian, CA Sotriffer - Journal of chemical information and …, 2013 - ACS Publications
A major shortcoming of empirical scoring functions for protein–ligand complexes is the low
degree of correlation between predicted and experimental binding affinities, as frequently …
degree of correlation between predicted and experimental binding affinities, as frequently …
[HTML][HTML] Learning protein-ligand binding affinity with atomic environment vectors
Scoring functions for the prediction of protein-ligand binding affinity have seen renewed
interest in recent years when novel machine learning and deep learning methods started to …
interest in recent years when novel machine learning and deep learning methods started to …
[HTML][HTML] Scoring functions for protein-ligand binding affinity prediction using structure-based deep learning: a review
The rapid and accurate in silico prediction of protein-ligand binding free energies or binding
affinities has the potential to transform drug discovery. In recent years, there has been a …
affinities has the potential to transform drug discovery. In recent years, there has been a …
Featurization strategies for protein–ligand interactions and their applications in scoring function development
The predictive performance of classical scoring functions (SFs) seems to have reached a
plateau. Currently, SFs relying on sophisticated machine learning techniques have shown …
plateau. Currently, SFs relying on sophisticated machine learning techniques have shown …
BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction
Motivation The identification of compound–protein interactions (CPIs) is an essential step in
the process of drug discovery. The experimental determination of CPIs is known for a large …
the process of drug discovery. The experimental determination of CPIs is known for a large …
Binding Affinity Prediction for Protein–Ligand Complexes Based on β Contacts and B Factor
Accurate determination of protein–ligand binding affinity is a fundamental problem in
biochemistry useful for many applications including drug design and protein–ligand docking …
biochemistry useful for many applications including drug design and protein–ligand docking …