Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges
SY Huang - Briefings in bioinformatics, 2018 - academic.oup.com
Protein–ligand docking has been playing an important role in modern drug discovery. To
model drug–target binding in real systems, a number of flexible-ligand docking algorithms …
model drug–target binding in real systems, a number of flexible-ligand docking algorithms …
Deep learning in drug design: protein-ligand binding affinity prediction
Computational drug design relies on the calculation of binding strength between two
biological counterparts especially a chemical compound, ie, a ligand, and a protein …
biological counterparts especially a chemical compound, ie, a ligand, and a protein …
Does a more precise chemical description of protein–ligand complexes lead to more accurate prediction of binding affinity?
PJ Ballester, A Schreyer… - Journal of chemical …, 2014 - ACS Publications
Predicting the binding affinities of large sets of diverse molecules against a range of
macromolecular targets is an extremely challenging task. The scoring functions that attempt …
macromolecular targets is an extremely challenging task. The scoring functions that attempt …
Incorporating explicit water molecules and ligand conformation stability in machine-learning scoring functions
Structure-based drug design is critically dependent on accuracy of molecular docking
scoring functions, and there is of significant interest to advance scoring functions with …
scoring functions, and there is of significant interest to advance scoring functions with …
[HTML][HTML] Efficient and accurate large library ligand docking with KarmaDock
Ligand docking is one of the core technologies in structure-based virtual screening for drug
discovery. However, conventional docking tools and existing deep learning tools may suffer …
discovery. However, conventional docking tools and existing deep learning tools may suffer …
Low-quality structural and interaction data improves binding affinity prediction via random forest
Docking scoring functions can be used to predict the strength of protein-ligand binding. It is
widely believed that training a scoring function with low-quality data is detrimental for its …
widely believed that training a scoring function with low-quality data is detrimental for its …
Performance of machine-learning scoring functions in structure-based virtual screening
Classical scoring functions have reached a plateau in their performance in virtual screening
and binding affinity prediction. Recently, machine-learning scoring functions trained on …
and binding affinity prediction. Recently, machine-learning scoring functions trained on …
Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power
Z Wang, H Sun, X Yao, D Li, L Xu, Y Li… - Physical Chemistry …, 2016 - pubs.rsc.org
As one of the most popular computational approaches in modern structure-based drug
design, molecular docking can be used not only to identify the correct conformation of a …
design, molecular docking can be used not only to identify the correct conformation of a …
KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
Accurately predicting protein–ligand binding affinities is an important problem in
computational chemistry since it can substantially accelerate drug discovery for virtual …
computational chemistry since it can substantially accelerate drug discovery for virtual …
Improving AutoDock Vina using random forest: the growing accuracy of binding affinity prediction by the effective exploitation of larger data sets
There is a growing body of evidence showing that machine learning regression results in
more accurate structure‐based prediction of protein‐ligand binding affinity. Docking …
more accurate structure‐based prediction of protein‐ligand binding affinity. Docking …