3 citations · 7 across the 10 of their papers we have counts for
10 papers
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…
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…
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…
The connection between polymer collapse and the onset of jamming
Alex T. Grigas, Aliza Fisher, Mark D. Shattuck +1
Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-a…
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…
Current MD forcefields fail to capture key features of protein structure and fluctuations: A case study of cyclophilin A and T4 lysozyme
Zhe Mei, Alex T. Grigas, John D. Treado +6
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of…
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…