Deep learning for advancing peptide drug development: Tools and methods in structure prediction and design

X Wu, H Lin, R Bai, H Duan - European Journal of Medicinal Chemistry, 2024 - Elsevier
Peptides can bind challenging disease targets with high affinity and specificity, offering
enormous opportunities for addressing unmet medical needs. However, peptides' unique …

Leak proof PDBBind: A reorganized dataset of protein-ligand complexes for more generalizable binding affinity prediction

J Li, X Guan, O Zhang, K Sun, Y Wang, D Bagni… - arXiv preprint arXiv …, 2023 - arxiv.org
Many physics-based and machine-learned scoring functions (SFs) used to predict protein-
ligand binding free energies have been trained on the PDBBind dataset. However, it is …

Prediction of Drug-Target Binding Affinity Based on Deep Learning Models

H Zhang, X Liu, W Cheng, T Wang, Y Chen - Computers in Biology and …, 2024 - Elsevier
The prediction of drug-target binding affinity (DTA) plays an important role in drug discovery.
Computerized virtual screening techniques have been used for DTA prediction, greatly …

Benchmarking Active Learning Protocols for Ligand-Binding Affinity Prediction

R Gorantla, A Kubincova, B Suutari… - Journal of Chemical …, 2024 - ACS Publications
Active learning (AL) has become a powerful tool in computational drug discovery, enabling
the identification of top binders from vast molecular libraries. To design a robust AL protocol …

Guided docking as a data generation approach facilitates structure-based machine learning on kinases

M Backenköhler, J Groß, V Wolf… - Journal of Chemical …, 2024 - ACS Publications
Drug discovery pipelines nowadays rely on machine learning models to explore and
evaluate large chemical spaces. While including 3D structural information is considered …

Machine Learning in Bio-cheminformatics

KM Merz, GW Wei, F Zhu - Journal of Chemical Information and …, 2024 - ACS Publications
In recent years, the application of machine learning (ML), including deep learning (DL), has
experienced exponential growth, which has promoted data-driven discovery in diverse …

Do molecular fingerprints identify diverse active drugs in large-scale virtual screening?(no)

V Venkatraman, J Gaiser, D Demekas, A Roy, R Xiong… - bioRxiv, 2022 - biorxiv.org
Computational approaches for small-molecule drug discovery now regularly scale to
consideration of libraries containing billions of candidate small molecules. One promising …