Protein fragment library

In order to reduce the conformational space, one can use protein fragment libraries rather than explicitly model every phi-psi angle.

Fragments are short segments of the peptide backbone, typically from 5 to 15 residues long, and do not include the side chains.

[6] This approach operates under the assumption that local interactions play a large role in stabilizing the overall protein conformation.

In any short sequence, the molecular forces constrain the structure, leading to only a small number of possible conformations, which can be modeled by fragments.

First, a representative subset of the PDB is chosen which should cover a diverse array of structures, preferably at a good resolution.

[7] Because the fragments are derived from structures that exist in nature, the segment of backbone they represent will have realistic bonding geometries.

This requires more computational work than deriving a sequence-independent fragment library but can potentially produce more accurate models.

Typically, the alpha helices and beta sheets are threaded against a template structure, but the loops in between are not specified and need to be predicted.

Additionally, for any fixed L, the diversity of structures capable of being modeled decreases as the length of the fragments increases.

Shorter fragments are more capable of covering the diverse array of structures found in the PDB than longer ones.