587 citations · 1.4k across the 36 of their papers we have counts for
36 papers
Prompt Engineering for Transformer-based Chemical Similarity Search Identifies Structurally Distinct Functional Analogues
Clayton W. Kosonocky, Aaron L. Feller, Claus O. Wilke +1
Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to com…
colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes
Achim Zeileis, Jason C. Fisher, Kurt Hornik +5
The R package colorspace provides a flexible toolbox for selecting individual colors or color palettes, manipulating these colors, and employing them in statistical graphics and da…
Dissecting the roles of local packing density and longer-range effects in protein sequence evolution
Amir Shahmoradi, Claus Wilke
What are the structural determinants of protein sequence evolution? A number of site-specific structural characteristics have been proposed, most of which are broadly related to ei…
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…
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…
Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors
Stephanie J. Spielman, Claus O. Wilke
We have investigated the influence of the plasma membrane environment on the molecular evolution of G protein-coupled receptors (GPCRs), the largest receptor family in Metazoa. In…