A comparative assessment of ranking accuracies of conventional and machine-learning-based scoring functions for protein-ligand binding affinity prediction
HM Ashtawy, NR Mahapatra - IEEE/ACM Transactions on …, 2012 - ieeexplore.ieee.org
Accurately predicting the binding affinities of large sets of protein-ligand complexes
efficiently is a key challenge in computational biomolecular science, with applications in …
efficiently is a key challenge in computational biomolecular science, with applications in …
The Impact of Data on Structure-Based Binding Affinity Predictions Using Deep Neural Networks
PY Libouban, S Aci-Sèche, JC Gómez-Tamayo… - International Journal of …, 2023 - mdpi.com
Artificial intelligence (AI) has gained significant traction in the field of drug discovery, with
deep learning (DL) algorithms playing a crucial role in predicting protein–ligand binding …
deep learning (DL) algorithms playing a crucial role in predicting protein–ligand binding …
graphDelta: MPNN scoring function for the affinity prediction of protein–ligand complexes
In this work, we present graph-convolutional neural networks for the prediction of binding
constants of protein–ligand complexes. We derived the model using multi task learning …
constants of protein–ligand complexes. We derived the model using multi task learning …
GraphLambda: fusion graph neural networks for binding affinity prediction
G Mqawass, P Popov - Journal of Chemical Information and …, 2024 - ACS Publications
Predicting the binding affinity of protein–ligand complexes is crucial for computer-aided drug
discovery (CADD) and the identification of potential drug candidates. The deep learning …
discovery (CADD) and the identification of potential drug candidates. The deep learning …
SS-GNN: a simple-structured graph neural network for affinity prediction
S Zhang, Y Jin, T Liu, Q Wang, Z Zhang, S Zhao… - ACS …, 2023 - ACS Publications
Efficient and effective drug-target binding affinity (DTBA) prediction is a challenging task due
to the limited computational resources in practical applications and is a crucial basis for drug …
to the limited computational resources in practical applications and is a crucial basis for drug …
Graphkan: Graph kolmogorov arnold network for small molecule-protein interaction predictions
This study presents a proof of concept for utilizing Graph Kolmogorov Arnold Networks
(GraphKAN/GKAN) in predicting the binding affinity of small molecules to protein targets …
(GraphKAN/GKAN) in predicting the binding affinity of small molecules to protein targets …
From proteins to ligands: decoding deep learning methods for binding affinity prediction
Accurate in silico prediction of protein–ligand binding affinity is important in the early stages
of drug discovery. Deep learning-based methods exist but have yet to overtake more …
of drug discovery. Deep learning-based methods exist but have yet to overtake more …
SQM2. 20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes
Accurate estimation of protein–ligand binding affinity is the cornerstone of computer-aided
drug design. We present a universal physics-based scoring function, named SQM2. 20 …
drug design. We present a universal physics-based scoring function, named SQM2. 20 …
Machine learning-based scoring functions, development and applications with SAnDReS
G Bitencourt-Ferreira, C Rizzotto… - Current medicinal …, 2021 - ingentaconnect.com
Background: Analysis of atomic coordinates of protein-ligand complexes can provide three-
dimensional data to generate computational models to evaluate binding affinity and …
dimensional data to generate computational models to evaluate binding affinity and …
Calibrated geometric deep learning improves kinase–drug binding predictions
Protein kinases regulate various cellular functions and hold significant pharmacological
promise in cancer and other diseases. Although kinase inhibitors are one of the largest …
promise in cancer and other diseases. Although kinase inhibitors are one of the largest …