System and method for accelerating FEP methods using a 3D-restricted variational autoencoder
US11568961B2 · kind B2 · utility
Assignee
Inventors
Key dates
| Filing date | May 31, 2022 |
| Grant date | Jan 31, 2023 |
| Priority date | — |
| Expiry date | May 31, 2042 |
Classification
- Technology area (CPC G)Physics
- CPC primaryG06V30/10
- WIPO fieldComputer technology
- WIPO sectorElectrical engineering
Abstract
A system and method for accelerating the calculations of free energy differences by automating FEP-path-decision-making and replacing the standard series of alchemical interpolations typically created by molecular dynamic (MD) simulations with voxelated interpolated states. A novel machine learning approach comprising a restricted variational autoencoder (ResVAE) is used which can reduce the computational-cost associated with interpolations by restricting the dimensions of a molecular latent space. The ResVAE generates a model based on flow-based transformations of a 3D-VAE latent point that is trained to maximize the log-likelihood of MD samples which enables the model to compute transformations more efficiently between molecules and also handle deletions of atoms more efficiently during iterative FEP calculation steps.
Source: USPTO / EPO open patent data. Objective bibliographic and citation counts.