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Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Protein Organization

RNA Structure

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

RNA Structure

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...

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Related Experiment Video

Updated: Apr 10, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

The trRosettaRNA server for RNA structure prediction.

Wenkai Wang¹, Xiaocheng Liu¹, Zhenling Peng¹

¹MOE Frontiers Science Center for Nonlinear Expectations, State Key Laboratory of Cryptography and Digital Economy Security, Shandong Province Key Laboratory of Financial Risk, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.

Nature Protocols

|April 8, 2026

Summary

This summary is machine-generated.

trRosettaRNA is a deep learning-based server for automated RNA 3D structure prediction. It offers high accuracy and flexibility, aiding research in understanding RNA functions and structures.

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Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

RNA molecules fold into complex three-dimensional (3D) structures essential for their biological functions, analogous to proteins.
Accurate prediction of these RNA 3D structures is crucial for understanding their roles in cellular processes.

Purpose of the Study:

To introduce trRosettaRNA, a novel web-based platform for automated RNA 3D structure prediction utilizing deep learning.
To provide researchers with a tool for accurate and efficient prediction of RNA tertiary structures.

Main Methods:

Development of an end-to-end deep learning neural network for direct RNA 3D structure prediction from nucleotide sequences.
Integration of optional inputs for custom multiple sequence alignments and secondary structures to enhance prediction accuracy.
Inclusion of an energy optimization step to refine predicted structures and resolve potential violations.

Main Results:

The trRosettaRNA server demonstrates state-of-the-art modeling accuracy for RNA 3D structure prediction.
Predictions for RNA families lacking known 3D structures showed high confidence and good agreement with experimental data.
Median prediction time for a 200-nucleotide RNA sequence is approximately 1 hour using 5 CPU cores.

Conclusions:

trRosettaRNA offers a powerful, accurate, and user-friendly solution for automated RNA 3D structure prediction.
The availability of both a web server and an open-source standalone package enhances accessibility, data privacy, and customization for diverse research needs.
trRosettaRNA facilitates advancements in understanding RNA structure-function relationships and enables the development of new bioinformatics tools.