Related papers: Molecular Conformation Generation via Shifting Sco…

Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a…

Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previous methods usually first predict the interatomic distances,…

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…

Diffusion-based generative models in SE(3)-invariant space have demonstrated promising performance in molecular conformation generation, but typically require solving stochastic differential equations (SDEs) with thousands of update steps.…

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular…

Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D \textit{de novo} generation), has become a fundamental task in drug designs. Existing diffusion-based 3D molecule generation methods could suffer from…

Predicting molecular conformations from molecular graphs is a fundamental problem in cheminformatics and drug discovery. Recently, significant progress has been achieved with machine learning approaches, especially with deep generative…

Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…

Molecular conformation generation poses a significant challenge in the field of computational chemistry. Recently, Diffusion Probabilistic Models (DPMs) and Score-Based Generative Models (SGMs) are effectively used due to their capacity for…

Molecule generation is a very important practical problem, with uses in drug discovery and material design, and AI methods promise to provide useful solutions. However, existing methods for molecule generation focus either on 2D graph…

Molecules are frequently represented as graphs, but the underlying 3D molecular geometry (the locations of the atoms) ultimately determines most molecular properties. However, most molecules are not static and at room temperature adopt a…

Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one…

A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…

Estimating three-dimensional conformations of a molecular graph allows insight into the molecule's biological and chemical functions. Fast generation of valid conformations is thus central to molecular modeling. Recent advances in…

Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to…

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…

Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…

Fast and accurate generation of molecular conformers is desired for downstream computational chemistry and drug discovery tasks. Currently, training and sampling state-of-the-art diffusion or flow-based models for conformer generation…

We present a novel way to predict molecular conformers through a simple formulation that sidesteps many of the heuristics of prior works and achieves state of the art results by using the advantages of scale. By training a diffusion…