# Guided Multi-objective Generative AI to Enhance Structure-based Drug Design

arXiv: https://arxiv.org/abs/2405.11785 · HTML: https://mlsanity.com/paper/2405.11785/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 28 of its 76 references that are in the map.
- First posted on arXiv 20 May 2024.

## Builds on (most cited first, 28 of 28)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [RePaint: Inpainting using Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2201.09865/) (2022)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [Tune: A Research Platform for Distributed Model Selection and Training](https://mlsanity.com/paper/1807.05118/) (2018)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [The Open Catalyst 2020 (OC20) Dataset and Community Challenges](https://mlsanity.com/paper/2010.09990/) (2020)
- [Structure-based Drug Design with Equivariant Diffusion Models](https://mlsanity.com/paper/2210.13695/) (2022)
- [Optimal rates for zero-order convex optimization: the power of two function evaluations](https://mlsanity.com/paper/1312.2139/) (2013)
- [Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets](https://mlsanity.com/paper/2205.07249/) (2022)
- [3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction](https://mlsanity.com/paper/2303.03543/) (2023)
- [A 3D Generative Model for Structure-Based Drug Design](https://mlsanity.com/paper/2203.10446/) (2022)
- [Generating 3D Molecules for Target Protein Binding](https://mlsanity.com/paper/2204.09410/) (2022)
- [Exploring Chemical Space with Score-based Out-of-distribution Generation](https://mlsanity.com/paper/2206.07632/) (2022)
- [The Open Catalyst 2022 (OC22) Dataset and Challenges for Oxide Electrocatalysts](https://mlsanity.com/paper/2206.08917/) (2022)
- [Inverse design of 3d molecular structures with conditional generative neural networks](https://mlsanity.com/paper/2109.04824/) (2021)
- [Less is more: sampling chemical space with active learning](https://mlsanity.com/paper/1801.09319/) (2018)
- [Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models](https://mlsanity.com/paper/2110.15200/) (2021)
- [The Synthesizability of Molecules Proposed by Generative Models](https://mlsanity.com/paper/2002.07007/) (2020)
- [DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding](https://mlsanity.com/paper/2211.11214/) (2022)
- [Learning to design drug-like molecules in three-dimensional space using deep generative models](https://mlsanity.com/paper/2104.08474/) (2021)
- [Do Deep Learning Models Really Outperform Traditional Approaches in Molecular Docking?](https://mlsanity.com/paper/2302.07134/) (2023)
- [STRIDE: Structure-guided Generation for Inverse Design of Molecules](https://mlsanity.com/paper/2311.06297/) (2023)

## Built on by (most cited first, 3 of 3)

- [Human-level molecular optimization driven by mol-gene evolution](https://mlsanity.com/paper/2406.12910/) (2024)
- [Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design](https://mlsanity.com/paper/2606.00555/) (2026)
- [DiffGA: Steering Frozen Diffusion Models for Materials Design via Evolutionary Search](https://mlsanity.com/paper/2610.14999/) (2026)

## Abstract (arXiv)

Generative AI has the potential to revolutionize drug discovery. Yet, despite recent advances in deep learning, existing models cannot generate molecules that satisfy all desired physicochemical properties. Herein, we describe IDOLpro, a generative chemistry AI combining diffusion with multi-objective optimization for structure-based drug design. Differentiable scoring functions guide the latent variables of the diffusion model to explore uncharted chemical space and generate novel ligands in silico, optimizing a plurality of target physicochemical properties. We demonstrate our platform's effectiveness by generating ligands with optimized binding affinity and synthetic accessibility on two benchmark sets. IDOLpro produces ligands with binding affinities over 10%-20% better than the next best state-of-the-art method on each test set, producing more drug-like molecules with generally better synthetic accessibility scores than other methods. We do a head-to-head comparison of IDOLpro against a classic virtual screen of a large database of drug-like molecules. We show that IDOLpro can generate molecules for a range of important disease-related targets with better binding affinity and synthetic accessibility than any molecule found in the virtual screen while being over 100x faster and less expensive to run. On a test set of experimental complexes, IDOLpro is the first to produce molecules with better binding affinities than experimentally observed ligands. IDOLpro can accommodate other scoring functions (e.g. ADME-Tox) to accelerate hit-finding, hit-to-lead, and lead optimization for drug discovery.