Predicting Folding Dynamics

Predicting Folding Dynamics

Predicting Folding Dynamics

Computational studies of protein have provided many important insights. But, such folding simulations nearly always require knowledge of the native state or some added heuristics. How this knowledge is implemented may bias the simulations in a manner that influences the outcome.

We have developed a new coarse-grained molecular dynamics (MD) package, Upside, which can reversibly fold some proteins up to 97 AA to under 4 Å RMSD in cpu days without the use of fragments, homology, or evolution. The source code for Upside is available for download from GitHub at the link below.

Approach

  • Upside utilizes a number of unique features, including rapid side chain packing that enables MD simulations with only 3 backbone atoms whilre retaining considerable detail and avoiding sidechain "rattling", which greatly slows standard all-atom methods.
  • We will continue to improve Upside and implement enhanced sampling methods to improve our accuracy and range of protein sizes

Links:

Download source code for Upside from GitHub