Protein–ligand docking in the machine-learning era
Molecular docking plays a significant role in early-stage drug discovery, from structure-
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …
Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term
Scoring functions are important components in molecular docking for structure-based drug
discovery. Traditional scoring functions, generally empirical-or force field-based, are robust …
discovery. Traditional scoring functions, generally empirical-or force field-based, are robust …
From machine learning to deep learning: Advances in scoring functions for protein–ligand docking
Molecule docking has been regarded as a routine tool for drug discovery, but its accuracy
highly depends on the reliability of scoring functions (SFs). With the rapid development of …
highly depends on the reliability of scoring functions (SFs). With the rapid development of …
Task-specific scoring functions for predicting ligand binding poses and affinity and for screening enrichment
HM Ashtawy, NR Mahapatra - Journal of chemical information and …, 2018 - ACS Publications
Molecular docking, scoring, and virtual screening play an increasingly important role in
computer-aided drug discovery. Scoring functions (SFs) are typically employed to predict the …
computer-aided drug discovery. Scoring functions (SFs) are typically employed to predict the …
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 …
DeepBSP—a machine learning method for accurate prediction of protein–ligand docking structures
J Bao, X He, JZH Zhang - Journal of chemical information and …, 2021 - ACS Publications
In recent years, machine-learning-based scoring functions have significantly improved the
scoring power. However, many of these methods do not perform well in distinguishing the …
scoring power. However, many of these methods do not perform well in distinguishing the …
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 …
Structural protein–ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study
C Da, D Kireev - Journal of chemical information and modeling, 2014 - ACS Publications
Accurate and affordable assessment of ligand–protein affinity for structure-based virtual
screening (SB-VS) is a standing challenge. Hence, empirical postdocking filters making use …
screening (SB-VS) is a standing challenge. Hence, empirical postdocking filters making use …
Improving scoring‐docking‐screening powers of protein–ligand scoring functions using random forest
The development of new protein–ligand scoring functions using machine learning
algorithms, such as random forest, has been of significant interest. By efficiently utilizing …
algorithms, such as random forest, has been of significant interest. By efficiently utilizing …
Beware of Machine Learning-Based Scoring Functions On the Danger of Developing Black Boxes
Training machine learning algorithms with protein–ligand descriptors has recently gained
considerable attention to predict binding constants from atomic coordinates. Starting from a …
considerable attention to predict binding constants from atomic coordinates. Starting from a …