David E. Shaw

TL;DR: Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand to find the best docked pose using a model energy function that combines empirical and force-field-based terms.

TL;DR: A new force field, which is termed Amber ff99SB‐ILDN, exhibits considerably better agreement with the NMR data and is validated against a large set of experimental NMR measurements that directly probe side‐chain conformations.

TL;DR: This work presents several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current state-of-the-art codes, including a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time.

TL;DR: The overall results are the best reported to date, and the combination of an accurate all‐atom energy function, efficient methods for loop buildup and side‐chain optimization, and, especially for the longer loops, the hierarchical refinement protocol is attributed.

TL;DR: Results of atomic-level molecular dynamics simulations of 12 proteins reveal a set of common principles underlying the folding of 12 structurally diverse proteins that spontaneously and repeatedly fold to their experimentally determined native structures.