Open-source machine learning in computational chemistry
A Hagg, KN Kirschner - Journal of Chemical Information and …, 2023 - ACS Publications
The field of computational chemistry has seen a significant increase in the integration of
machine learning concepts and algorithms. In this Perspective, we surveyed 179 open …
machine learning concepts and algorithms. In this Perspective, we surveyed 179 open …
Application of variational graph encoders as an effective generalist algorithm in computer-aided drug design
Although there has been considerable progress in molecular property prediction in
computer-aided drug design, there is a critical need to have fast and accurate models. Many …
computer-aided drug design, there is a critical need to have fast and accurate models. Many …
Developments in molecular docking technologies for application of polysaccharide-based materials: A review
R Lin, J Zhang, R Xu, C Yuan, L Guo, P Liu… - Critical Reviews in …, 2023 - Taylor & Francis
With the increasing pollution of the planet, the search for natural multifunctional alternatives
to petroleum-based plastics has assumed to be a great important proposition …
to petroleum-based plastics has assumed to be a great important proposition …
[HTML][HTML] CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training
The expertise accumulated in deep neural network-based structure prediction has been
widely transferred to the field of protein–ligand binding pose prediction, thus leading to the …
widely transferred to the field of protein–ligand binding pose prediction, thus leading to the …
[HTML][HTML] PIGNet2: a versatile deep learning-based protein–ligand interaction prediction model for binding affinity scoring and virtual screening
Prediction of protein–ligand interactions (PLI) plays a crucial role in drug discovery as it
guides the identification and optimization of molecules that effectively bind to target proteins …
guides the identification and optimization of molecules that effectively bind to target proteins …
Water network-augmented two-state model for protein–ligand binding affinity prediction
X Qu, L Dong, D Luo, Y Si, B Wang - Journal of Chemical …, 2023 - ACS Publications
Water network rearrangement from the ligand-unbound state to the ligand-bound state is
known to have significant effects on the protein–ligand binding interactions, but most of the …
known to have significant effects on the protein–ligand binding interactions, but most of the …
Computational chemistry in structure-based solute carrier transporter drug design: Recent advances and future perspectives
G Tu, T Fu, G Zheng, B Xu, R Gou, D Luo… - Journal of chemical …, 2024 - ACS Publications
Solute carrier transporters (SLCs) are a class of important transmembrane proteins that are
involved in the transportation of diverse solute ions and small molecules into cells. There are …
involved in the transportation of diverse solute ions and small molecules into cells. There are …
A systematic survey in geometric deep learning for structure-based drug design
Structure-based drug design (SBDD), which utilizes the three-dimensional geometry of
proteins to identify potential drug candidates, is becoming increasingly vital in drug …
proteins to identify potential drug candidates, is becoming increasingly vital in drug …
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15
We introduce a deep learning‐based ligand pose scoring model called zPoseScore for
predicting protein–ligand complexes in the 15th Critical Assessment of Protein Structure …
predicting protein–ligand complexes in the 15th Critical Assessment of Protein Structure …
A versatile deep learning-based protein-ligand interaction prediction model for accurate binding affinity scoring and virtual screening
Protein--ligand interaction (PLI) prediction is critical in drug discovery, aiding the
identification and enhancement of molecules that effectively bind to target proteins. Despite …
identification and enhancement of molecules that effectively bind to target proteins. Despite …