FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries

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Förster resonance energy transfer (FRET) is a widely-used and versatile technique for the structural characterization of biomolecules. Here, we introduce FRETpredict, an easy-to-use Python software to predict FRET efficiencies from ensembles of protein conformations. FRETpredict uses a rotamer library approach to describe the FRET probes covalently bound to the protein. The software efficiently and flexibly operates on large conformational ensembles such as those generated by molecular dynamics simulations to facilitate the validation or refinement of molecular models and the interpretation of experimental data. We provide access to rotamer libraries for many commonly used dyes and linkers and describe a general methodology to generate new rotamer libraries for FRET probes. We demonstrate the performance and accuracy of the software for different types of systems: a rigid peptide (polyproline 11), an intrinsically disordered protein (ACTR), and three folded proteins (HiSiaP, SBD2, and MalE). FRETpredict is open source (GPLv3) and is available at github.com/KULL-Centre/FRETpredict and as a Python PyPI package at pypi.org/project/FRETpredict.
OriginalsprogEngelsk
Artikelnummer298
TidsskriftCommunications Biology
Vol/bind7
Udgave nummer1
Antal sider10
ISSN2399-3642
DOI
StatusUdgivet - 2024

Bibliografisk note

Funding Information:
M.B.A.K. acknowledges funding from the Lundbeck Foundation (lundbeckfonden.com). K.L.-L. acknowledges funding via a Sapere Aude Starting Grant from the Danish Council for Independent Research (Natur og Univers, Det Frie Forskningsråd, 12-126214, https://dff.dk/) and the Lundbeck Foundation BRAINSTRUC initiative in structural biology (R155-2015-2666, lundbeckfonden.com). We acknowledge the use of resources at the core facility for biocomputing at the Department of Biology. R.B.B. was supported by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health. This work utilized the computational resources of the NIH HPC Biowulf cluster. (http://hpc.nih.gov).

Publisher Copyright:
© The Author(s) 2024.

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