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.
- Content Type Journal Article
- Category Article
- Pages 1-11
- DOI 10.1007/s10858-012-9632-7
- Authors
- Georg Kontaxis, Max F. Perutz Laboratories, Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
Source: Journal of Biomolecular NMR