Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions
New drug production, from target identification to marketing approval, takes over 12 years
and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the …
and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the …
[HTML][HTML] Exploring the computational methods for protein-ligand binding site prediction
J Zhao, Y Cao, L Zhang - Computational and structural biotechnology …, 2020 - Elsevier
Proteins participate in various essential processes in vivo via interactions with other
molecules. Identifying the residues participating in these interactions not only provides …
molecules. Identifying the residues participating in these interactions not only provides …
Yuel: Improving the generalizability of structure-free compound–protein interaction prediction
J Wang, NV Dokholyan - Journal of chemical information and …, 2022 - ACS Publications
Predicting binding affinities between small molecules and the protein target is at the core of
computational drug screening and drug target identification. Deep learning-based …
computational drug screening and drug target identification. Deep learning-based …
[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, several deep learning …
affinities has the potential to transform drug discovery. In recent years, several deep learning …
DEELIG: A deep learning approach to predict protein-ligand binding affinity
Protein-ligand binding prediction has extensive biological significance. Binding affinity helps
in understanding the degree of protein-ligand interactions and is a useful measure in drug …
in understanding the degree of protein-ligand interactions and is a useful measure in drug …
[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …
molecules. Thus, one may obtain biological insights into protein functions, disease …
Statistical and machine learning approaches to predicting protein–ligand interactions
LJ Colwell - Current opinion in structural biology, 2018 - Elsevier
Data driven computational approaches to predicting protein–ligand binding are currently
achieving unprecedented levels of accuracy on held-out test datasets. Up until now …
achieving unprecedented levels of accuracy on held-out test datasets. Up until now …
[HTML][HTML] Deciphering protein–protein interactions. Part II. Computational methods to predict protein and domain interaction partners
BA Shoemaker, AR Panchenko - PLoS computational biology, 2007 - journals.plos.org
Recent advances in high-throughput experimental methods for the identification of protein
interactions have resulted in a large amount of diverse data that are somewhat incomplete …
interactions have resulted in a large amount of diverse data that are somewhat incomplete …
[HTML][HTML] A brief review of protein–ligand interaction prediction
The task of identifying protein–ligand interactions (PLIs) plays a prominent role in the field of
drug discovery. However, it is infeasible to identify potential PLIs via costly and laborious in …
drug discovery. However, it is infeasible to identify potential PLIs via costly and laborious in …
Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions
Accurately predicting protein–ligand binding affinities can substantially facilitate the drug
discovery process, but it remains as a difficult problem. To tackle the challenge, many …
discovery process, but it remains as a difficult problem. To tackle the challenge, many …