Inverse design of 3d molecular structures with conditional generative
neural networks
- URL: http://arxiv.org/abs/2109.04824v1
- Date: Fri, 10 Sep 2021 12:12:38 GMT
- Title: Inverse design of 3d molecular structures with conditional generative
neural networks
- Authors: Niklas W. A. Gebauer, Michael Gastegger, Stefaan S. P. Hessmann,
Klaus-Robert M\"uller, Kristof T. Sch\"utt
- Abstract summary: We propose a conditional generative neural network for 3d molecular structures with specified structural and chemical properties.
This approach is agnostic to chemical bonding and enables targeted sampling of novel molecules from conditional distributions.
- Score: 2.7998963147546148
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: The rational design of molecules with desired properties is a long-standing
challenge in chemistry. Generative neural networks have emerged as a powerful
approach to sample novel molecules from a learned distribution. Here, we
propose a conditional generative neural network for 3d molecular structures
with specified structural and chemical properties. This approach is agnostic to
chemical bonding and enables targeted sampling of novel molecules from
conditional distributions, even in domains where reference calculations are
sparse. We demonstrate the utility of our method for inverse design by
generating molecules with specified composition or motifs, discovering
particularly stable molecules, and jointly targeting multiple electronic
properties beyond the training regime.
Related papers
- Molecule Design by Latent Space Energy-Based Modeling and Gradual
Distribution Shifting [53.44684898432997]
Generation of molecules with desired chemical and biological properties is critical for drug discovery.
We propose a probabilistic generative model to capture the joint distribution of molecules and their properties.
Our method achieves very strong performances on various molecule design tasks.
arXiv Detail & Related papers (2023-06-09T03:04:21Z) - Towards Predicting Equilibrium Distributions for Molecular Systems with
Deep Learning [60.02391969049972]
We introduce a novel deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems.
DiG employs deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system.
arXiv Detail & Related papers (2023-06-08T17:12:08Z) - MUDiff: Unified Diffusion for Complete Molecule Generation [104.7021929437504]
We present a new model for generating a comprehensive representation of molecules, including atom features, 2D discrete molecule structures, and 3D continuous molecule coordinates.
We propose a novel graph transformer architecture to denoise the diffusion process.
Our model is a promising approach for designing stable and diverse molecules and can be applied to a wide range of tasks in molecular modeling.
arXiv Detail & Related papers (2023-04-28T04:25:57Z) - DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding [51.970607704953096]
Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one by one.
In real-world molecular systems, the interactions among atoms in an entire molecule are global, leading to the energy function pair-coupled among atoms.
In this work, a generative diffusion model for molecular 3D structures based on target proteins is established, at a full-atom level in a non-autoregressive way.
arXiv Detail & Related papers (2022-11-21T07:02:15Z) - Substructure-Atom Cross Attention for Molecular Representation Learning [21.4652884347198]
We propose a new framework for molecular representation learning.
Our contribution is threefold: (a) demonstrating the usefulness of incorporating substructures to node-wise features from molecules, (b) designing two branch networks consisting of a transformer and a graph neural network, and (c) not requiring features and computationally-expensive information from molecules.
arXiv Detail & Related papers (2022-10-15T09:44:27Z) - Exploring Chemical Space with Score-based Out-of-distribution Generation [57.15855198512551]
We propose a score-based diffusion scheme that incorporates out-of-distribution control in the generative differential equation (SDE)
Since some novel molecules may not meet the basic requirements of real-world drugs, MOOD performs conditional generation by utilizing the gradients from a property predictor.
We experimentally validate that MOOD is able to explore the chemical space beyond the training distribution, generating molecules that outscore ones found with existing methods, and even the top 0.01% of the original training pool.
arXiv Detail & Related papers (2022-06-06T06:17:11Z) - Scalable Fragment-Based 3D Molecular Design with Reinforcement Learning [68.8204255655161]
We introduce a novel framework for scalable 3D design that uses a hierarchical agent to build molecules.
In a variety of experiments, we show that our agent, guided only by energy considerations, can efficiently learn to produce molecules with over 100 atoms.
arXiv Detail & Related papers (2022-02-01T18:54:24Z) - Generating 3D Molecules Conditional on Receptor Binding Sites with Deep
Generative Models [0.0]
We describe for the first time a deep learning system for generating 3D molecular structures conditioned on a receptor binding site.
We apply atom fitting and bond inference procedures to construct valid molecular conformations from generated atomic densities.
This work opens the door for end-to-end prediction of stable bioactive molecules from protein structures with deep learning.
arXiv Detail & Related papers (2021-10-28T15:17:24Z) - Learning a Continuous Representation of 3D Molecular Structures with
Deep Generative Models [0.0]
Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous latent space.
We describe deep generative models of three dimensional molecular structures using atomic density grids.
We are also able to sample diverse sets of molecules based on a given input compound to increase the probability of creating valid, drug-like molecules.
arXiv Detail & Related papers (2020-10-17T01:15:47Z) - Generating 3D Molecular Structures Conditional on a Receptor Binding
Site with Deep Generative Models [0.0]
We describe for the first time a deep generative model that can generate 3D structures conditioned on a three-dimensional molecular binding pocket.
We show that valid and unique molecules can be readily sampled from the variational latent space defined by a reference seed' structure.
arXiv Detail & Related papers (2020-10-16T16:27:47Z) - Multi-Objective Molecule Generation using Interpretable Substructures [38.637412590671865]
Drug discovery aims to find novel compounds with specified chemical property profiles.
The goal is to learn to sample molecules in the intersection of multiple property constraints.
We propose to offset this complexity by composing molecules from a vocabulary of substructures that we call molecular rationales.
arXiv Detail & Related papers (2020-02-08T22:55:37Z)
This list is automatically generated from the titles and abstracts of the papers in this site.
This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.