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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…
Core packing of well-defined x-ray and NMR structures is the same
Alex T. Grigas, Zhuoyi Liu, Lynne Regan +1
Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by x-ray crystallography…
Using physical features of protein core packing to distinguish real proteins from decoys
Alex T. Grigas, Zhe Mei, John D. Treado +3
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein struc…
Analyses of protein cores reveal fundamental differences between solution and crystal structures
Zhe Mei, John D. Treado, Alex T. Grigas +3
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of th…
Void distributions reveal structural link between jammed packings and protein cores
John D. Treado, Zhe Mei, Lynne Regan +1
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $ϕ\approx 0.…
Random close packing in protein cores
Jennifer C. Gaines, W. Wendell Smith, Lynne Regan +1
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions , a value that is simi…