3 papers
q-bio.BM2026
Assessment of scoring functions for computational models of protein-protein interfaces
Jacob Sumner, Grace Meng, Naomi Brandt +4
A goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this probl…
cond-mat.soft2025
The effect of stereochemical constraints on the structural properties of folded proteins
Jack A. Logan, Jacob Sumner, Alex T. Grigas +2
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino aci…
cs.LG2024
ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
Siddharth Viswanath, Dhananjay Bhaskar, David R. Johnson +7
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static fold…