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Related Experiment Video

Updated: Aug 4, 2025

Interactive Molecular Model Assembly with 3D Printing

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

Deep generative models for 3D molecular structure.

Benoit Baillif¹, Jason Cole², Patrick McCabe²

¹Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Rd, CB2 1EW, Cambridge, United Kingdom.

Current Opinion in Structural Biology

|March 31, 2023

Summary

This summary is machine-generated.

Explicit 3D molecular generative models are emerging for chemical design, generating molecules with atom types and coordinates. While promising for structure-based design, challenges remain in efficiency and conformational realism.

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3D Printing of Biomolecular Models for Research and Pedagogy

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

Area of Science:

Computational chemistry
Drug discovery
Artificial intelligence in chemistry

Background:

Deep generative models are increasingly popular for chemical design.
Historically, these models operated in 2D, but explicit 3D molecular generation is a recent focus.
Dozens of 3D generative models have been developed, outputting atom types and coordinates.

Purpose of the Study:

To review and discuss explicit 3D molecular generative models for chemical design.
To highlight the capabilities and limitations of current 3D generative models.
To propose a unified benchmark for evaluating generation and suggest future research directions.

Main Methods:

Review of published explicit 3D molecular generative models.
Analysis of model outputs, including atom types and coordinates.
Evaluation of model performance in terms of docking scores, efficiency, and conformational realism.

Main Results:

3D generative models can generate molecules with docking scores comparable to known actives when guided by structural information.
These models exhibit lower computational efficiency and generation throughput compared to 1D/2D models.
Current 3D models may produce unrealistic molecular conformations.

Conclusions:

Explicit 3D generative models show significant potential for structure-based chemical design.
Further research is needed to improve computational efficiency and conformational accuracy.
A unified benchmark is crucial for standardized evaluation and advancement of these models.