Related papers: Learning 3D Representations of Molecular Chirality…

Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utilizing graph neural network (GNN) parametrizations, with…

Chirality is a fundamental molecular property that governs stereospecific behavior in chemistry and biology. Capturing chirality in machine learning models remains challenging due to the geometric complexity of stereochemical relationships…

Molecules with identical graph connectivity can exhibit different physical and biological properties if they exhibit stereochemistry-a spatial structural characteristic. However, modern neural architectures designed for learning…

Graph Neural Networks (GNNs) play a fundamental role in many deep learning problems, in particular in cheminformatics. However, typical GNNs cannot capture the concept of chirality, which means they do not distinguish between the 3D graph…

Molecular shape and geometry dictate key biophysical recognition processes, yet many graph neural networks disregard 3D information for molecular property prediction. Here, we propose a new contrastive-learning procedure for graph neural…

Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of…

Virtual screening can accelerate drug discovery by identifying promising candidates for experimental evaluation. Machine learning is a powerful method for screening, as it can learn complex structure-property relationships from experimental…

A molecule's 2D representation consists of its atoms, their attributes, and the molecule's covalent bonds. A 3D (geometric) representation of a molecule is called a conformer and consists of its atom types and Cartesian coordinates. Every…

Molecular property prediction, crucial for early drug candidate screening and optimization, has seen advancements with deep learning-based methods. While deep learning-based methods have advanced considerably, they often fall short in fully…

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D…

Chirality is a fundamental feature in all domains of nature, ranging from particle physics over electromagnetism to chemistry and biology. Chiral objects lack a mirror plane and inversion symmetry and therefore cannot be spatially aligned…

Graph neural networks (GNNs) have achieved remarkable success in molecular property prediction. However, traditional graph representations struggle to effectively encode the inherent 3D spatial structures of molecules, as molecular…

Molecular chirality is a geometric property that is of great importance in chemistry, biology, and medicine. Recently, plasmonic nanostructures that exhibit distinct chiroptical responses have attracted tremendous interest, given their…

Deep learning is changing many areas in molecular physics, and it has shown great potential to deliver new solutions to challenging molecular modeling problems. Along with this trend arises the increasing demand of expressive and versatile…

The fundamental issues of symmetry related to chirality are discussed and applied to simple situations relevant to liquid crystals. We show that any chiral measure of a geometric object is a pseudoscalar (invariant under proper rotations…

Locally Rotation Invariant (LRI) image analysis was shown to be fundamental in many applications and in particular in medical imaging where local structures of tissues occur at arbitrary rotations. LRI constituted the cornerstone of several…

The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update atom and molecule features from the fed atom (and, in some…

Circular dichroism spectroscopy is an essential technique for understanding molecular structure and magnetic materials, but spatial resolution is limited by the wavelength of light, and sensitivity sufficient for single-molecule…

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

Chirality is of primary importance in many areas of chemistry and has been extensively investigated since its discovery. We introduce here the description of central chirality for tetrahedral molecules using a geometrical approach based on…