Evidence map›Paper›PMID 41856113›Full record

ArticleCell2026

Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.

Ainan Geng, Rohit Roy, Megan Ken, Linshu Li, Alicia Chime, Hala Abou Assi, Bei Liu, Charles Bou-Nader, Yeongjoon Lee, Jinwei Zhang and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Ainan GengDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
Rohit RoyCenter for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.
Megan KenDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
Linshu LiDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Alicia ChimeDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Hala Abou AssiDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
Bei LiuDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
Charles Bou-NaderLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
Yeongjoon LeeDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Jinwei ZhangLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
Daniel HerschlagDepartment of Biochemistry, Stanford University, Stanford, CA, USA.
Stephen P GoffDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Hashim M Al-HashimiDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. Electronic address: ha2639@cumc.columbia.edu.

Funding

The Center for HIV RNA Studies (CRNA)U54AI150470 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI TELESNITSKY, ALICE · 2019 to 2021
$15.1M
RM1 Center on Macromolecular Dynamics by NMR Spectroscopy at the New York Structural Biology Center (CoMD/NMR)- Equipment Supplement RequestRM1GM145397 · NIGMS · NEW YORK STRUCTURAL BIOLOGY CENTER · PI ARTHUR G PALMER · 2022 to 2026
$8.3M
Development and application of a quantitive model for HIV-1 transcriptional activation driven by TAR RNA conformational dynamicsR01AI178848 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Hashim M Al-Hashimi, STEPHEN Paine GOFF · 2023 to 2026
$3.2M
475 MHz NMR SpectrometerS10OD023499 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI PALMER, ARTHUR G · 2017 to 2017
$925k
Upgrade of 800 MHz SpectrometerS10OD016432 · OD · NEW YORK STRUCTURAL BIOLOGY CENTER · PI PALMER, ARTHUR G · 2014 to 2014
$600k
Acquisition of an 800 MHz TXO CryoProbeS10OD028577 · OD · NEW YORK STRUCTURAL BIOLOGY CENTER · PI PALMER, ARTHUR G · 2020 to 2020
$299k
NIAID NIH HHS R01 AI178848NIAID NIH HHS U54 AI150470NIGMS NIH HHS RM1 GM145397NIH HHS S10 OD016432NIH HHS S10 OD023499NIH HHS S10 OD028577
6 · The paper itself

Abstract

Despite advances in structure prediction from sequence, predicting cellular activity requires conformational ensembles that capture propensities to form functionally active states. Such ensembles remain difficult to measure and even harder to predict. Here, we systematically altered the HIV-1 transactivation response element (TAR) RNA sequence to change its propensity to adopt a functional versus inactive secondary structure and quantified these propensities using proton chemical exchange saturation transfer (

Indexed as

HIV-1RNA, ViralHIV Long Terminal RepeatHumansNucleic Acid Conformationtat Gene Products, Human Immunodeficiency VirusThermodynamicsRNA, Viraltat Gene Products, Human Immunodeficiency VirusAlphaFoldconformational propensitiesHIV-1 TARpredicting conformational ensemblesRNA secondary structure prediction

Identifiers

PMID41856113
PMCPMC13270807

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.