Genomic landscape of advanced prostate cancer patients with versus mutations as detected by comprehensive genomic profiling of cell-free DNA.

-mutated prostate cancer has been shown to be less responsive to poly (ADP-ribose) polymerase (PARP) inhibitors as compared to -mutated prostate cancer. The reason for this differential response is not clear. We hypothesized this differential sensitivity to PARP inhibitors may be explained by distinct genomic landscapes of versus co-segregating genes.

Small-molecule ligand docking into comparative models with Rosetta.

Structure-based drug design is frequently used to accelerate the development of small-molecule therapeutics. Although substantial progress has been made in X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, the availability of high-resolution structures is limited owing to the frequent inability to crystallize or obtain sufficient NMR restraints for large or flexible proteins. Computational methods can be used to both predict unknown protein structures and model ligand interactions when experimental data are unavailable.

Practically useful: what the Rosetta protein modeling suite can do for you.

The objective of this review is to enable researchers to use the software package Rosetta for biochemical and biomedicinal studies. We provide a brief review of the six most frequent research problems tackled with Rosetta. For each of these six tasks, we provide a tutorial that illustrates a basic Rosetta protocol.

Predicting the sensitivity and specificity of published real-time PCR assays.

Background: In recent years real-time PCR has become a leading technique for nucleic acid detection and quantification. These assays have the potential to greatly enhance efficiency in the clinical laboratory. Choice of primer and probe sequences is critical for accurate diagnosis in the clinic, yet current primer/probe signature design strategies are limited, and signature evaluation methods are lacking.