Ab initio

Seeks to predict the native conformation of a protein from the amino acid sequence alone.

Simplifications: to employ implicit solvent models, united atom representations, side chains represented using a limited set of conformations found prevalent in PDB, restricting the conformation available to the polypeptide backbone.

Rosetta: based on a model of folding in which short segments of the protein chain flicker between different local structures, consistent with their local sequences, and folding to the native state occurs when these local segments are oriented such that low free energy interactions are made throughout the protein.


Two categories of potential functions can be employed in evaluating the free energy of the peptide chain and the surrounding solvent: molecular mechanics and protein-structure derived potentials or scoring functions derived from experimental structures from the PDB.