An improved algorithm for MFR fragment assembly.

Journal of Biomolecular NMR
Georg Kontaxis

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.

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Citations

Jan 1, 2021·The Journal of Chemical Physics·Justin T Seffernick, Steffen Lindert
Jan 1, 2018·Progress in Nuclear Magnetic Resonance Spectroscopy·Santrupti NerliNikolaos G Sgourakis
Sep 5, 2019·ACS Central Science·Justin T SeffernickSteffen Lindert

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