Drugclip: Contrasive protein-molecule representation learning for virtual screening

B Gao, B Qiang, H Tan, Y Jia, M Ren… - Advances in …, 2024 - proceedings.neurips.cc
Virtual screening, which identifies potential drugs from vast compound databases to bind
with a particular protein pocket, is a critical step in AI-assisted drug discovery. Traditional …

[HTML][HTML] Accelerating high-throughput virtual screening through molecular pool-based active learning

DE Graff, EI Shakhnovich, CW Coley - Chemical science, 2021 - pubs.rsc.org
Structure-based virtual screening is an important tool in early stage drug discovery that
scores the interactions between a target protein and candidate ligands. As virtual libraries …

[HTML][HTML] Virtual Screening with Gnina 1.0

J Sunseri, DR Koes - Molecules, 2021 - mdpi.com
Virtual screening—predicting which compounds within a specified compound library bind to
a target molecule, typically a protein—is a fundamental task in the field of drug discovery …

[HTML][HTML] SCORCH: Improving structure-based virtual screening with machine learning classifiers, data augmentation, and uncertainty estimation

M McGibbon, S Money-Kyrle, V Blay… - Journal of Advanced …, 2023 - Elsevier
Introduction The discovery of a new drug is a costly and lengthy endeavour. The
computational prediction of which small molecules can bind to a protein target can …

Machine‐learning scoring functions for structure‐based virtual screening

H Li, KH Sze, G Lu, PJ Ballester - Wiley Interdisciplinary …, 2021 - Wiley Online Library
Molecular docking predicts whether and how small molecules bind to a macromolecular
target using a suitable 3D structure. Scoring functions for structure‐based virtual screening …

Lean-docking: exploiting ligands' predicted docking scores to accelerate molecular docking

F Berenger, A Kumar, KYJ Zhang… - Journal of Chemical …, 2021 - ACS Publications
In structure-based virtual screening (SBVS), a binding site on a protein structure is used to
search for ligands with favorable nonbonded interactions. Because it is computationally …

[HTML][HTML] Deepbindgcn: Integrating molecular vector representation with graph convolutional neural networks for protein–ligand interaction prediction

H Zhang, KM Saravanan, JZH Zhang - Molecules, 2023 - mdpi.com
The core of large-scale drug virtual screening is to select the binders accurately and
efficiently with high affinity from large libraries of small molecules in which non-binders are …

Boosting protein–ligand binding pose prediction and virtual screening based on residue–atom distance likelihood potential and graph transformer

C Shen, X Zhang, Y Deng, J Gao, D Wang… - Journal of Medicinal …, 2022 - ACS Publications
The past few years have witnessed enormous progress toward applying machine learning
approaches to the development of protein–ligand scoring functions. However, the robust …

Predicting protein–ligand docking structure with graph neural network

H Jiang, J Wang, W Cong, Y Huang… - Journal of chemical …, 2022 - ACS Publications
Modern day drug discovery is extremely expensive and time consuming. Although
computational approaches help accelerate and decrease the cost of drug discovery, existing …

Data set augmentation allows deep learning-based virtual screening to better generalize to unseen target classes and highlight important binding interactions

J Scantlebury, N Brown, F Von Delft… - Journal of chemical …, 2020 - ACS Publications
Current deep learning methods for structure-based virtual screening take the structures of
both the protein and the ligand as input but make little or no use of the protein structure …