English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Plus monthly

Global: Zendy Tools annual

Global: Zendy Tools monthly

Global: Zendy Free Plan

To address the large gap between time scales that can be easily reached bymolecular simulations and those required to understand protein dynamics, wepropose a rapid self-consistent approximation of the side chain free energy atevery integration step. In analogy with the adiabatic Born-Oppenheimerapproximation for electronic structure, the protein backbone dynamics aresimulated as preceding according to the dictates of the free energy of aninstantaneously-equilibrated side chain potential. The side chain free energyis computed on the fly, allowing the protein backbone dynamics to traverse agreatly smoothed energetic landscape. This results in extremely rapidequilibration and sampling of the Boltzmann distribution. Because our methodemploys a reduced model involving single-bead side chains, we also provide anovel, maximum-likelihood method to parameterize the side chain model usinginput data from high resolution protein crystal structures. We demonstratestate-of-the-art accuracy for predicting $\chi_1$ rotamer states whileconsuming only milliseconds of CPU time. We also show that the resulting freeenergies of side chains is sufficiently accurate for de novo folding of someproteins.

Rapid calculation of side chain packing and free energy with applications to protein molecular dynamics