Upside v1.0.0

Initial public release. Stable in terms of core functionality.

Trajectory Training Paper

Corresponds to the state of the code used to produce the work in: Jumper JM, Faruk NF, Freed KF, Sosnick TR (2018) Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours. PLoS Comput Biol 14(12): e1006578. https://doi.org/10.1371/journal.pcbi.1006578

Sidechain Packing Paper

Corresponds to the state of the code used to produce the work in: Jumper JM, Faruk NF, Freed KF, Sosnick TR (2018) Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics. PLoS Comput Biol 14(12): e1006342. https://doi.org/10.1371/journal.pcbi.1006342