November 2023

Journal

TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences

By:
Hsu, Darren J; Lu, Hao ; Kashi, Aditya ; Matheson, Michael A; Gounley, John P; Wang, Feiyi ; Joubert, Wayne D; Glaser, Jens-Steffen
Journal Name:
The International Journal of High Performance Computing Applications
Page Number:
XX-XX
Volume:
Online 1st
Issue Number:
Online 1st
Publication Date:
November 2023
View DOI Listing:
https://doi.org/10.1177/10943420231201151

Abstract

We describe our development of ab initio protein-ligand binding pose prediction models based on transformers and binding affinity prediction models based on the neural tangent kernel (NTK). Folding both protein and ligand, the TwoFold models achieve efficient and quality predictions matching state-of-the-art implementations while additionally reconstructing protein structures. Solving NTK models points to a new use case for highly optimized linear solver benchmarking codes on HPC.