Improving scoring‐docking‐screening powers of protein–ligand scoring functions using random forest

C Wang, Y Zhang - Journal of computational chemistry, 2017 - Wiley Online Library
The development of new protein–ligand scoring functions using machine learning
algorithms, such as random forest, has been of significant interest. By efficiently utilizing …

Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results

Y Li, L Han, Z Liu, R Wang - Journal of chemical information and …, 2014 - ACS Publications
Our comparative assessment of scoring functions (CASF) benchmark is created to provide
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …

Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term

L Zheng, J Meng, K Jiang, H Lan, Z Wang… - Briefings in …, 2022 - academic.oup.com
Scoring functions are important components in molecular docking for structure-based drug
discovery. Traditional scoring functions, generally empirical-or force field-based, are robust …

Delta machine learning to improve scoring-ranking-screening performances of protein–ligand scoring functions

C Yang, Y Zhang - Journal of chemical information and modeling, 2022 - ACS Publications
Protein–ligand scoring functions are widely used in structure-based drug design for fast
evaluation of protein–ligand interactions, and it is of strong interest to develop scoring …

Comparative assessment of scoring functions on an updated benchmark: 1. Compilation of the test set

Y Li, Z Liu, J Li, L Han, J Liu, Z Zhao… - Journal of chemical …, 2014 - ACS Publications
Scoring functions are often applied in combination with molecular docking methods to
predict ligand binding poses and ligand binding affinities or to identify active compounds …

Comparative assessment of scoring functions: the CASF-2016 update

M Su, Q Yang, Y Du, G Feng, Z Liu, Y Li… - Journal of chemical …, 2018 - ACS Publications
In structure-based drug design, scoring functions are often employed to evaluate protein–
ligand interactions. A variety of scoring functions have been developed so far, and thus …

Tapping on the black box: how is the scoring power of a machine-learning scoring function dependent on the training set?

M Su, G Feng, Z Liu, Y Li, R Wang - Journal of chemical …, 2020 - ACS Publications
In recent years, protein–ligand interaction scoring functions derived through machine-
learning are repeatedly reported to outperform conventional scoring functions. However …

ID-Score: a new empirical scoring function based on a comprehensive set of descriptors related to protein–ligand interactions

GB Li, LL Yang, WJ Wang, LL Li… - Journal of chemical …, 2013 - ACS Publications
Scoring functions have been widely used to assess protein–ligand binding affinity in
structure-based drug discovery. However, currently commonly used scoring functions face …

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 …

Featurization strategies for protein–ligand interactions and their applications in scoring function development

G Xiong, C Shen, Z Yang, D Jiang, S Liu… - Wiley …, 2022 - Wiley Online Library
The predictive performance of classical scoring functions (SFs) seems to have reached a
plateau. Currently, SFs relying on sophisticated machine learning techniques have shown …