Related papers: Learning a Continuous Representation of 3D Molecul…
Deep generative models have been applied with increasing success to the generation of two dimensional molecules as SMILES strings and molecular graphs. In this work we describe for the first time a deep generative model that can generate 3D…
The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to…
Deep learning has proven to yield fast and accurate predictions of quantum-chemical properties to accelerate the discovery of novel molecules and materials. As an exhaustive exploration of the vast chemical space is still infeasible, we…
The de novo design of molecular structures using deep learning generative models introduces an encouraging solution to drug discovery in the face of the continuously increased cost of new drug development. From the generation of original…
We study a fundamental problem in structure-based drug design -- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are…
Generative models aim to learn the distribution of observed data by generating new instances. With the advent of neural networks, deep generative models, including variational autoencoders (VAEs), generative adversarial networks (GANs), and…
In the space of only a few years, deep generative modeling has revolutionized how we think of artificial creativity, yielding autonomous systems which produce original images, music, and text. Inspired by these successes, researchers are…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…
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…
Structure-based drug design involves finding ligand molecules that exhibit structural and chemical complementarity to protein pockets. Deep generative methods have shown promise in proposing novel molecules from scratch (de-novo design),…
With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based…
Deep generative models have recently been applied to molecule design. If the molecules are encoded in linear SMILES strings, modeling becomes convenient. However, models relying on string representations tend to generate invalid samples and…
Recently, deep generative models for molecular graphs are gaining more and more attention in the field of de novo drug design. A variety of models have been developed to generate topological structures of drug-like molecules, but…
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…
Deep generative models have emerged as a powerful tool for learning useful molecular representations and designing novel molecules with desired properties, with applications in drug discovery and material design. However, most existing deep…
Probabilistic generative deep learning for molecular design involves the discovery and design of new molecules and analysis of their structure, properties and activities by probabilistic generative models using the deep learning approach.…
Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…
Designing new chemical compounds with desired pharmaceutical properties is a challenging task and takes years of development and testing. Still, a majority of new drugs fail to prove efficient. Recent success of deep generative modeling…
Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…
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…