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Updated: May 6, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

Raktim Mitra¹, Ari S Cohen¹, Wei Yu Tang¹

¹Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

Journal of Molecular Biology

|March 24, 2025

Summary

This summary is machine-generated.

RNAproDB is a new webserver and database for analyzing protein-nucleic acid complexes. It offers visualization tools and computes structural annotations to reveal molecular binding patterns.

Keywords:

DNA structure RNA structure molecular recognition nucleic acids protein-nucleic acid binding

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Last Updated: May 6, 2026

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Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

Protein-nucleic acid interactions are fundamental to numerous biological processes.
Analyzing these complexes requires specialized tools for visualization and data interpretation.
Existing resources may not comprehensively cover diverse nucleic acid structures and interaction types.

Purpose of the Study:

To introduce RNAproDB, a comprehensive webserver and database for protein-nucleic acid complexes.
To provide advanced analysis and visualization tools for exploring these structures.
To facilitate the study of molecular binding and recognition patterns in protein-RNA interactions.

Main Methods:

Development of a webserver, analysis pipeline, and interactive database.
Computation of multiple mapping schemes for nucleic acid components and protein-RNA interactions.
Inclusion of structural annotations such as base-pairing geometries, hydrogen bonds, and water-mediated interactions.
Integration of visualization tools, including subgraph selection and electrostatic potential mapping.

Main Results:

RNAproDB provides a platform for analyzing experimentally determined, predicted, and designed protein-nucleic acid complexes.
The tool computes detailed structural annotations and interaction information.
Quantitative analysis of pre-analyzed structures reveals statistical patterns in molecular binding and recognition.

Conclusions:

RNAproDB serves as a valuable resource for researchers studying protein-nucleic acid complexes.
The integrated analysis and visualization capabilities enhance the exploration of molecular interactions.
The database facilitates the discovery of general principles governing molecular recognition in these systems.