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.
J.M. Jumper, K.F. Freed, T.R. Sosnick, "Trajectory-Based Parameterization of a Coarse-Grained Forcefield for High-Throughput Protein Simulation" bioRxiv:169326.
J.M. Jumper, K.F. Freed, T.R. Sosnick, "Maximum-likelihood, self-consistent side chain free energies with applications to protein molecular dynamics" arXiv:1610.07277 [q-bio.BM].