Transformers for molecular property prediction: Lessons learned from the past five years
Molecular Property Prediction (MPP) is vital for drug discovery, crop protection, and
environmental science. Over the last decades, diverse computational techniques have been …
environmental science. Over the last decades, diverse computational techniques have been …
Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry
PE Bowling, DR Broderick… - Journal of Chemical Theory …, 2024 - ACS Publications
Fragment-based quantum chemistry methods offer a means to sidestep the steep nonlinear
scaling of electronic structure calculations so that large molecular systems can be …
scaling of electronic structure calculations so that large molecular systems can be …
Predicting the binding of small molecules to proteins through invariant representation of the molecular structure
R Beccaria, A Lazzeri, G Tiana - Journal of Chemical Information …, 2024 - ACS Publications
We present a computational scheme for predicting the ligands that bind to a pocket of a
known structure. It is based on the generation of a general abstract representation of the …
known structure. It is based on the generation of a general abstract representation of the …
Augmented BindingNet dataset for enhanced ligand binding pose predictions using deep learning
H Zhu, X Li, B Chen, N Huang - npj Drug Discovery, 2025 - nature.com
High-quality data on protein-ligand complex structures and binding affinities are crucial for
structure-based drug design. Existing datasets often lack diversity and quantity, limiting the …
structure-based drug design. Existing datasets often lack diversity and quantity, limiting the …
GEMS: A Generalizable GNN Framework For Protein-Ligand Binding Affinity Prediction Through Robust Data Filtering and Language Model Integration
The field of computational drug design requires accurate scoring functions to predict binding
affinities for protein-ligand interactions. However, train-test data leakage between the …
affinities for protein-ligand interactions. However, train-test data leakage between the …
Quantum Mechanical Approaches for Large Protein Systems: Fragmentation, Confining Potentials, and Anisotropic Solvation
P Bowling - 2024 - search.proquest.com
Fragment-based quantum chemistry methods provide a way to circumvent the steep
nonlinear scaling of electronic structure calculations, enabling the investigation of large …
nonlinear scaling of electronic structure calculations, enabling the investigation of large …