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 …
new drug development, represents a major threat to human health. In order to reduce the …
Geometric deep learning for structure-based ligand design
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 …
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
Ensemble docking can be a successful virtual screening technique that addresses the
innate conformational heterogeneity of macromolecular drug targets. Yet, lacking a method …
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 …
binding of small molecules to proteins have been developed. Their objective is to …
AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening
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 …
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
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 …
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 …
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
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 …
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 …
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
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 …
However, as the chemical space expands, the existing structure-based virtual screening …