Raw data and data accompanying publication: https://doi.org/10.1261/rna.080367.124

Raw data and data accompanying publication:

Angelo M., Bhargava Y., Kierzek E., Kierzek R., Hayes R.L., Zhang W., Vilseck J.Z., Aoki S.T., Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics. RNA (2025) 31(10), 1460-1471. https://doi.org/10.1261/rna.080367.124

Authors: 
Murphy Angelo (1), Yash Bhargava (1), Elzbieta Kierzek (2), Ryszard Kierzek (2), Ryan L Hayes (3,4), Wen Zhang* (1,5), Jonah Z Vilseck* (1,6), Scott Takeo Aoki* (1,5)

Affiliation:
(1) Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
(2) Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
(3) Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697, USA
(4) Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, USA
(5) Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
(6) Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA

* Corresponding authors: E-mails: wz15@iu.edu, jvilseck@iu.edu, staoki@iu.edu

License:  CC BY-NC 4.0

This work was supported by: S.T.A., W.Z., and J.Z.V. received startup funds from the Indiana University School of Medicine and its Precision Health Initiative (PHI). J.Z.V. is funded by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) (R35GM146888). S.T.A. is funded by the NIH/NIGMS (R35GM142691) and an Indiana University Research Support Funds Grant (RSFG). E.K. is funded by UMO-2020/39/B/NZ1/03054 and R.K. is funded by UMO-2022/45/B/ST4/03586.

Contents:
Data1: Legends.
Data2: Figure S1- ANOVA binding statistics.
Data3: Figure S2- Human Pumilio 2 binding to modified RNAs.
Data4: Figure S3- A thermodynamic cycle used for computing relative binding free energies (ΔΔGbind).
Data5: Table S1- Human Pumilio 1 and 2 λ-dynamics screening results to unmodified RNA. 
Data6: Table S2- Human Pumilio 1 λ-dynamics screening results to modified RNA. 
Data7: Table S3- Human Pumilio 2 λ-dynamics and in vitro binding results to modified RNA. 
Data8: Table S4- Alchemical groups for initial λ-dynamics screen of modified RNA bases.