title: An improved algorithm for MFR fragment assembly.
abstract: A method for generating protein backbone models from backbone only NMR data is presented, which is based on molecular fragment replacement (MFR). In a first step, the PDB database is mined for homologous peptide fragments using experimental backbone-only data i.e. backbone chemical shifts (CS) and residual dipolar couplings (RDC). Second, this fragment library is refined against the experimental restraints. Finally, the fragments are assembled into a protein backbone fold using a rigid body docking algorithm using the RDCs as restraints. For improved performance, backbone nuclear Overhauser effects (NOEs) may be included at that stage. Compared to previous implementations of MFR-derived structure determination protocols this model-building algorithm offers improved stability and reliability. Furthermore, relative to CS-ROSETTA based methods, it provides faster performance and straightforward implementation with the option to easily include further types of restraints and additional energy terms.
authors.affiliation: Max F. Perutz Laboratories, Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria. georg.kontaxis@univie.ac.at
authors.forename: Georg
authors.initials: G
authors.lastname: Kontaxis
mesh_terms: D000465:Algorithms; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins