FRET Positioning and Screening (FPS)

A comprehensive toolkit for Förster resonance energy transfer (FRET) restrained modeling of biomolecules and their complexes for quantitative applications in structural biology. A dramatic improvement in the precision of FRET-derived structures is achieved by explicitly considering spatial distributions of dye positions, which greatly reduces uncertainties due to flexible dye linkers.The precision and confidence levels of the models are calculated by rigorous error estimation.The accuracy of this approach is demonstrated by docking a DNA primer-template to HIV-1 reverse transcriptase.The derived model agrees with the known X-ray structure with an r.m.s. deviation of 0.5 Å. Furthermore, we introduce FRET-guided ‘screening’ of a large structural ensemble created by molecular dynamics simulations. We used this hybrid approach to determine the formerly unknown configuration of the flexible single-strand template overhang

Download:
Program V1.1 (8 Mbyte), Test data (6 Mbyte), Dye parameters

Source code is available upon request (please briefly indicate your intentions)

Reference:
Kalinin, S., Peulen, T., Sindbert, S., Rothwell, P. J., Berger, S., Restle, T., Goody, R. S., Gohlke, H., and Seidel C. A. M. A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nat. Methods 9, [accepted 5.10.12; online, planned for 11.11.12; printed version in issue 12] (2012); doi: 10.1038/NMETH.2222

Verantwortlich für den Inhalt: E-Mail sendenProf. Dr. Claus Seidel