| Scientific / Technical Presentation | Vikram Mulligan | Previous work: Designing peptides of mixed L/D amino acids with unnatural folds Macrocycles Current software limitations Rosetta is a kinematics engine and a scoring engine Rosetta is very good at solving the rotamer optimization problem Predicted fold propensity (estimated dG of folding) correlated well with IC50 Mike Gilson: Mining Minima Enhancing Rosetta’s energy calculations with quantum chemistry Limitations of Rosetta as a platform for future science MPI-parallel but not GPU-parallel “Pose” data structure is optimized for side chain optimization, relaxation, and backbone sampling Rosetta is a monolith (software engineering perspective)
Designing and building the Masala software suite Usable as stand-alone or robust library Free and open source successor to Rosetta under development at Flatiron Structured to take advantage of massively parallel CPU or GPU Versatile plugin architecture Internal library API layer Plugins User interfaces
API layer is built from JSON API description Special types of Masala plugins Using Masala to implement packing on quantum computers
Hope to implement translator to and from OpenFF to set up force fields Option 1: Implement internal Masala representation of molecule and implement our own machinery to parameterize it with force field from offxml Option 2: Use OpenFF’s implementation (toolkit) to parameterize the system Option 3: Use Interchange to output in a different format
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