The latin term 'ab initio' is used in bioinformatics to describe methods used to predict protein structures without the benefit of homologs or any other information about the structure of a protein. With respect to protein structure prediction, ab initio means without prior knowledge.

Both homology and fold recognition approaches rely on the availability of template structures in the database to achieve predictions. If no correct structures exist in the database, the methods fail. However, proteins in nature fold on their own without checking what the structures of their homologs are in databases. Obviously, there is some information in the sequences that provides instruction for the proteins to “find” their native structures. Early biophysical studies have shown that most proteins fold spontaneously into a stable structure that has near minimum energy. This structural state is called the native state. This folding process appears to be nonrandom; however, its mechanism is poorly understood. The limited knowledge of protein folding forms the basis of ab initio prediction. As the name suggests, the ab initio prediction method attempts to produce all-atom protein models based on sequence information alone without the aid of known protein structures. The perceived advantage of this method is that predictions are not restricted by known folds and that novel protein folds can be identified. However, because the physicochemical laws governing protein folding are not yet well understood, the energy functions used in the ab initio prediction are at present rather inaccurate. The folding problem remains one of the greatest   challenges in bioinformatics today. Current ab initio algorithms are not yet able to accurately simulate the protein folding process. They work by using some type of heuristics. Because the native state of a protein structure is near energy minimum, the prediction programs are thus designed using the energy minimization principle. These algorithms search for every possible conformation to find the one with the lowest global energy. However, searching for a fold with the absolute minimum energy may not be valid in reality. This contributes to one of the fundamental flaws of this approach. In addition, searching for all possible structural conformations is not yet computationally feasible. It has been estimated that, by using one of the world’s fastest supercomputers (one trillion operations per second), it takes 1020 years to sample all possible conformations of a 40-residue protein. Therefore, some type of heuristics must be used to reduce the conformational space to be searched. Some recent ab initio methods combine fragment search and threading to yield a model of an unknown protein.

Rosetta is a web server that predicts protein three-dimensional conformations using the ab initio method. This in fact relies on a “mini-threading” method. The method first breaks down the query sequence into many very short segments (three to nine residues) and predicts the secondary structure of the small segments using a hidden Markov model–based program, HMMSTR. The segments with assigned secondary structures are subsequently assembled into a three-dimensional configuration. Through random combinations of the fragments, a large number of models are built and their overall energy potentials calculated. The conformation with the lowest global free energy is chosen as the best model.