A review of mathematical representations of biomolecular data
Recently, machine learning (ML) has established itself in various worldwide benchmarking
competitions in computational biology, including Critical Assessment of Structure Prediction …
competitions in computational biology, including Critical Assessment of Structure Prediction …
AGL-score: algebraic graph learning score for protein–ligand binding scoring, ranking, docking, and screening
Although algebraic graph theory-based models have been widely applied in physical
modeling and molecular studies, they are typically incompetent in the analysis and …
modeling and molecular studies, they are typically incompetent in the analysis and …
Algorithmic Graph Theory, Reinforcement Learning and Game Theory in MD Simulations: From 3D Structures to Topological 2D-Molecular Graphs (2D-MolGraphs) …
S Bougueroua, M Bricage, Y Aboulfath, D Barth… - Molecules, 2023 - mdpi.com
This paper reviews graph-theory-based methods that were recently developed in our group
for post-processing molecular dynamics trajectories. We show that the use of algorithmic …
for post-processing molecular dynamics trajectories. We show that the use of algorithmic …
GGL-Tox: geometric graph learning for toxicity prediction
Toxicity analysis is a major challenge in drug design and discovery. Recently significant
progress has been made through machine learning due to its accuracy, efficiency, and lower …
progress has been made through machine learning due to its accuracy, efficiency, and lower …
MathDL: mathematical deep learning for D3R Grand Challenge 4
We present the performances of our mathematical deep learning (MathDL) models for D3R
Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free …
Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free …
Liquid structure of a choline chloride-water natural deep eutectic solvent: A molecular dynamics characterization
The liquid structure of a representative of the first water-in-salt (WiS) Natural Deep Eutectic
Solvents (NADES), hereinafter indicated as aquoline, a mixture of choline chloride (ChCl) …
Solvents (NADES), hereinafter indicated as aquoline, a mixture of choline chloride (ChCl) …
ReNeGate: A reaction network graph-theoretical tool for automated mechanistic studies in computational homogeneous catalysis
Exploration of the chemical reaction space of chemical transformations in multicomponent
mixtures is one of the main challenges in contemporary computational chemistry. To remove …
mixtures is one of the main challenges in contemporary computational chemistry. To remove …
Graph–theoretic analysis of monomethyl phosphate clustering in ionic solutions
K Han, RM Venable, AM Bryant… - The Journal of …, 2018 - ACS Publications
All-atom molecular dynamics simulations combined with graph–theoretic analysis reveal
that clustering of monomethyl phosphate dianion (MMP2–) is strongly influenced by the …
that clustering of monomethyl phosphate dianion (MMP2–) is strongly influenced by the …
Efficient and universal characterization of atomic structures through a topological graph order parameter
A graph-based order parameter, based on the topology of the graph itself, is introduced for
the characterization of atomistic structures. The order parameter is universal to any …
the characterization of atomistic structures. The order parameter is universal to any …
Design principles of PI(4,5)P2 clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy
Phosphatidylinositol 4, 5-bisphosphate (PIP2) clustering is a key component in cell
signaling, yet little is known about the atomic-level features of this phenomenon. Network …
signaling, yet little is known about the atomic-level features of this phenomenon. Network …