Protein fragment library
Protein backbone fragment libraries have been used successfully in a variety of structural biology applications, including homology modeling, structure prediction, structure determination, decoy detection, and … By reducing the complexity of the search space, these fragment libraries enable more rapid search of conformational space, leading to more efficient and accurate models.
Motivation
Proteins can adopt an exponential number of states when modeled discretely. Typically a protein’s conformations are represented as sets of dihedral angles, bond lengths, and bond angles between all connected atoms. The most common simplification is to assume ideal bond lengths and bond angles. However this still leaves the phi-psi angles of the backbone, and up to four dihedral angles for each side chain, leading to a worst case complexity of k6*n possible states of the protein, where n is the number of residues and k is the number of discrete states modeled for each dihedral angle.
In order to reduce the conformational space, one can use protein fragment libraries rather than explicitly model every phi-psi angle. Rather than model the full range of these dihedral angles, the most commonly found ones in the Protein Data Bank are used. Fragments are constructed from
Note, side chains are typically not modeled using the fragment library approach, but are modeled using rotamer libraries.
