# Sesame: Opening the door to protein pockets

arXiv: https://arxiv.org/abs/2509.05302 · HTML: https://mlsanity.com/paper/2509.05302/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 10 of its 41 references that are in the map.
- First posted on arXiv 21 Aug 2025.

## Builds on (most cited first, 10 of 10)

- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [Stochastic Interpolants: A Unifying Framework for Flows and Diffusions](https://mlsanity.com/paper/2303.08797/) (2023)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [A survey of the Schr"odinger problem and some of its connections with optimal transport](https://mlsanity.com/paper/1308.0215/) (2013)
- [Flow Matching on General Geometries](https://mlsanity.com/paper/2302.03660/) (2023)
- [SE(3)-Stochastic Flow Matching for Protein Backbone Generation](https://mlsanity.com/paper/2310.02391/) (2023)
- [AlphaFold Meets Flow Matching for Generating Protein Ensembles](https://mlsanity.com/paper/2402.04845/) (2024)
- [Improved motif-scaffolding with SE(3) flow matching](https://mlsanity.com/paper/2401.04082/) (2024)

## Built on by (most cited first, 1 of 1)

- [Fractional Diffusion Bridge Models](https://mlsanity.com/paper/2511.01795/) (2025)

## Abstract (arXiv)

Molecular docking is a cornerstone of drug discovery, relying on high-resolution ligand-bound structures to achieve accurate predictions. However, obtaining these structures is often costly and time-intensive, limiting their availability. In contrast, ligand-free structures are more accessible but suffer from reduced docking performance due to pocket geometries being less suited for ligand accommodation in apo structures. Traditional methods for artificially inducing these conformations, such as molecular dynamics simulations, are computationally expensive. In this work, we introduce Sesame, a generative model designed to predict this conformational change efficiently. By generating geometries better suited for ligand accommodation at a fraction of the computational cost, Sesame aims to provide a scalable solution for improving virtual screening workflows.