Damietta: a tensorized protein design engine

Damietta is a protein design framework that aims to achieve maximal acceleration of computation, while relying on a strictly physics-based energy function. Current version of the Damietta software includes 4 main routines: - (sp) the single point routine generates one or more mutations at a single amino acid position; - (ra) the repack all routine repacks the side chains of all amino acids along the structure once, from N- to C-terminus; - (spl) the single point library routine takes a series of conformations of the input protein (e.g. NMR model or molecular dynamics frames) and ranks the lowest average energy side chains across all models; - (cs_f2m2f) the combinatorial sampling few-to-many-to-few routine performs full-fledged fixed-backbone design allowing mutagenesis and side chain flexibility of any number of residues, and optimizes their energy combinatorially. The routine follows a few-to-many-to-few optimization strategy