1.6k citations · 6.6k across the 131 of their papers we have counts for
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ProtScape: A molecular structure and energy-aware representation for protein conformation generation
Siddharth Viswanath, Dhananjay Bhaskar, Xingzhi Sun +13
Molecular dynamics (MD) simulations are a principled but computationally expensive approach for studying protein conformational variability, making it challenging to generate large…
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…
Flow and clogging of capillary droplets
Yuxuan Cheng, Benjamin F. Lonial, Shivnag Sista +5
Capillary droplets form due to surface tension when two immiscible fluids are mixed. We describe the motion of gravity-driven capillary droplets flowing through narrow constriction…
Protein folding as a jamming transition
Alex T. Grigas, Zhuoyi Liu, Jack A. Logan +2
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins th…
Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling
Zhuoyi Liu, Alex T. Grigas, Jacob Sumner +3
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determ…
Gradient-based Design of Computational Granular Crystals
Atoosa Parsa, Corey S. O'Hern, Rebecca Kramer-Bottiglio +1
There is growing interest in engineering unconventional computing devices that leverage the intrinsic dynamics of physical substrates to perform fast and energy-efficient computati…