Evidence map›Paper›PMID 40126909›Full record

ArticleJournal of molecular biology2025

RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions.

Raktim Mitra, Ari S Cohen, Wei Yu Tang, Hirad Hosseini, Yongchan Hong, Helen M Berman, Remo Rohs

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Article
  2. Article
  3. A DNN Biophysics Model with Topological and Electrostatic Features.Journal of chemical information and modeling · 2026
    Article
  4. Article
  5. ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces.Computational and structural biotechnology journal · 2026
    Article
  6. Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025
    Article
  7. Article
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

7 authors.

Raktim MitraDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Ari S CohenDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Wei Yu TangDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Hirad HosseiniDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Yongchan HongDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Helen M BermanDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.
Remo RohsDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA; Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA; Department of Medicine, Division of Medical Oncology, University of Southern California, Los Angeles, CA 90033, USA. Electronic address: rohs@usc.edu.

Funding

Quantitative Modeling of Transcription Factor-DNA BindingR35GM130376 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI Remo Rohs · 2019 to 2026
$3.3M
NIGMS NIH HHS R35 GM130376
6 · The paper itself

Abstract

We present RNAproDB (https://rnaprodb.usc.edu/), a new webserver, analysis pipeline, database, and highly interactive visualization tool, designed for protein-RNA complexes, and applicable to all forms of nucleic acid containing structures. RNAproDB computes several mapping schemes to place nucleic acid components and present protein-RNA interactions appropriately. Various structural annotations are computed including non-canonical base-pairing geometries, hydrogen bonds, and protein-RNA and RNA-RNA water-mediated interactions. This information is presented through integrated visualization and data tools. Subgraph selection facilitates studying smaller components of the interface. Molecular surface electrostatic potential can be visualized. RNAproDB enables analyzing and exploring experimentally determined, predicted, and designed protein-nucleic acid complexes. We present a quantitative analysis of pre-analyzed protein-RNA structures in RNAproDB revealing statistical patterns of molecular binding and recognition.

Indexed as

DNA structuremolecular recognitionnucleic acidsprotein-nucleic acid bindingRNA structure

Identifiers

PMID40126909
PMCPMC12353319

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.