3 papers
physics.bio-ph2014
Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design
Amir Shahmoradi, Dariya K. Sydykova, Stephanie J. Spielman +4
Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts wit…
q-bio.BM2013
Analyzing Machupo virus-receptor binding by molecular dynamics simulations
Austin G. Meyer, Sara L. Sawyer, Andrew D. Ellington +1
In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein-protein interactions. However, many commonly used met…
q-bio.BM2012
Maximum allowed solvent accessibilites of residues in proteins
Matthew Z. Tien, Austin G. Meyer, Dariya K. Sydykova +2
The relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D structure. RSA is frequently used to describe…