Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings.

ABSTRACT: Residual Dipolar Couplings (RDCs) are a source of NMR data that can provide a powerful set of constraints on the orientation of inter-nuclear vectors, and are quickly becoming a larger part of the experimental toolset for molecular biologists. However, few reliable protocols exist for the determination of protein backbone structures from small sets of RDCs. DynaFold is a new dynamic programming algorithm designed specifically for this task, using minimal sets of RDCs collected in multiple alignment media. DynaFold was first tested utilizing synthetic data generated for the N--H , C(α)--H(α), and C--N vectors of 1BRF, 1F53, 110M, and 3LAY proteins, with up to ±1 Hz error in three alignment media, and was able to produce structures with less than 1.9 Å of the original structures. DynaFold wa

SUBMITTER: Mukhopadhyay R 

PROVIDER: S-EPMC4071617 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature