Brian G. Pierce

TL;DR: This paper presents a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers, and provides options for users to guide the scoring and the selection of output models.

TL;DR: An integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones.

TL;DR: A recently developed 3D convolution library is incorporated into ZDOCK, and the program is modified to dynamically orient the input proteins for more efficient convolution, resulting in an average of over 8.5-fold improvement in running time when tested on 176 cases in a newly released protein docking benchmark, as well as substantially less memory usage.

TL;DR: A scoring function that utilizes detailed electrostatics, van der Waals, and desolvation to rescore initial‐stage docking predictions is developed and tested and is shown to significantly improve the success rate over the initial ZDOCK rankings across a large benchmark.

TL;DR: This Perspective reviews tools developed over the past five years in the Rosetta software, including over 80 methods, and discusses improvements to the score function, user interfaces and usability.