RosENet: improving binding affinity prediction by leveraging molecular mechanics energies with an ensemble of 3D convolutional neural networks

H Hassan-Harrirou, C Zhang… - Journal of chemical …, 2020 - ACS Publications
The worldwide increase and proliferation of drug resistant microbes, coupled with the lag in
new drug development, represents a major threat to human health. In order to reduce the …

Geometric deep learning for structure-based ligand design

AS Powers, HH Yu, P Suriana, RV Koodli… - ACS Central …, 2023 - ACS Publications
A pervasive challenge in drug design is determining how to expand a ligand─ a small
molecule that binds to a target biomolecule─ in order to improve various properties of the …

Knowledge-based methods to train and optimize virtual screening ensembles

RV Swift, SA Jusoh, TL Offutt, ES Li… - Journal of chemical …, 2016 - ACS Publications
Ensemble docking can be a successful virtual screening technique that addresses the
innate conformational heterogeneity of macromolecular drug targets. Yet, lacking a method …

A small step toward generalizability: training a machine learning scoring function for structure-based virtual screening

J Scantlebury, L Vost, A Carbery… - Journal of Chemical …, 2023 - ACS Publications
Over the past few years, many machine learning-based scoring functions for predicting the
binding of small molecules to proteins have been developed. Their objective is to …

AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening

B Ni, H Wang, HKS Khalaf, V Blay… - Journal of Chemical …, 2024 - ACS Publications
Ligand-based virtual screening (LBVS) can be pivotal for identifying potential drug leads,
especially when the target protein's structure is unknown. However, current LBVS methods …

Generating 3D molecules conditional on receptor binding sites with deep generative models

M Ragoza, T Masuda, DR Koes - Chemical science, 2022 - pubs.rsc.org
The goal of structure-based drug discovery is to find small molecules that bind to a given
target protein. Deep learning has been used to generate drug-like molecules with certain …

Prediction of Molecular Conformation using Deep Generative Neural Networks

C Xu, Y Lu, X Deng, P Yu - Chinese Journal of Chemistry, 2023 - Wiley Online Library
The accurate prediction of molecular conformations with high efficiency is crucial in various
fields such as materials science, computational chemistry and computer‐aided drug design …

PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences

M Buttenschoen, GM Morris, CM Deane - Chemical Science, 2024 - pubs.rsc.org
The last few years have seen the development of numerous deep learning-based protein–
ligand docking methods. They offer huge promise in terms of speed and accuracy. However …

Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design

PG Francoeur, T Masuda, J Sunseri, A Jia… - Journal of chemical …, 2020 - ACS Publications
One of the main challenges in drug discovery is predicting protein–ligand binding affinity.
Recently, machine learning approaches have made substantial progress on this task …

Deep Learning with Geometry-Enhanced Molecular Representation for Augmentation of Large-Scale Docking-Based Virtual Screening

L Yu, X He, X Fang, L Liu, J Liu - Journal of Chemical Information …, 2023 - ACS Publications
Structure-based virtual screening has been a crucial tool in drug discovery for decades.
However, as the chemical space expands, the existing structure-based virtual screening …