[HTML][HTML] Structure-based protein–ligand interaction fingerprints for binding affinity prediction

DD Wang, MT Chan, H Yan - Computational and Structural Biotechnology …, 2021 - Elsevier
Binding affinity prediction (BAP) using protein–ligand complex structures is crucial to
computer-aided drug design, but remains a challenging problem. To achieve efficient and …

[HTML][HTML] Protein-ligand binding affinity prediction based on profiles of intermolecular contacts

DD Wang, MT Chan - Computational and Structural Biotechnology Journal, 2022 - Elsevier
As a key element in structure-based drug design, binding affinity prediction (BAP) for
putative protein-ligand complexes can be efficiently achieved by the incorporation of …

Proteo-chemometrics interaction fingerprints of protein–ligand complexes predict binding affinity

DD Wang, H Xie, H Yan - Bioinformatics, 2021 - academic.oup.com
Motivation Reliable predictive models of protein–ligand binding affinity are required in many
areas of biomedical research. Accurate prediction based on current descriptors or molecular …

SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors

S Kumar, M Kim - Journal of cheminformatics, 2021 - Springer
In drug discovery, rapid and accurate prediction of protein–ligand binding affinities is a
pivotal task for lead optimization with acceptable on-target potency as well as …

Extended connectivity interaction features: improving binding affinity prediction through chemical description

N Sánchez-Cruz, JL Medina-Franco, J Mestres… - …, 2021 - academic.oup.com
Motivation Machine-learning scoring functions (SFs) have been found to outperform
standard SFs for binding affinity prediction of protein–ligand complexes. A plethora of …

Scoring functions for protein-ligand binding affinity prediction using structure-based deep learning: a review

R Meli, GM Morris, PC Biggin - Frontiers in bioinformatics, 2022 - frontiersin.org
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 …

Iterative Knowledge-Based Scoring Function for Protein–Ligand Interactions by Considering Binding Affinity Information

X Zhao, H Li, K Zhang, SY Huang - The Journal of Physical …, 2023 - ACS Publications
Scoring functions for protein–ligand interactions play a critical role in structure-based drug
design. Owing to the good balance between general applicability and computational …

A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction

T Cheng, Z Liu, R Wang - BMC bioinformatics, 2010 - Springer
Background Current scoring functions are not very successful in protein-ligand binding
affinity prediction albeit their popularity in structure-based drug designs. Here, we propose a …

A comparative assessment of predictive accuracies of conventional and machine learning scoring functions for protein-ligand binding affinity prediction

HM Ashtawy, NR Mahapatra - IEEE/ACM transactions on …, 2014 - ieeexplore.ieee.org
Accurately predicting the binding affinities of large diverse sets of protein-ligand complexes
efficiently is a key challenge in computational biomolecular science, with applications in …

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 …