Philip Bradley

TL;DR: This chapter describes the requirements for the ROSETTA molecular modeling program's new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.

TL;DR: This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15), and explains how to use Rosetta energies to identify and analyze the features of biomolecular models.

TL;DR: The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology and the primary bottleneck to consistent high-resolution prediction appears to be conformational sampling.

TL;DR: Analytical tools developed develop a distance measure on the space of TCRs that permits clustering and visualization, a robust repertoire diversity metric that accommodates the low number of paired public receptors observed when compared to single-chain analyses, and a distance-based classifier that can assign previously unobserved T CRs to characterized repertoires with robust sensitivity and specificity.

TL;DR: The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization, and illustrates the basis of TAL effector–DNA recognition.