Related Experiment Video
Updated: May 21, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PRince: a web server for structural and physicochemical analysis of protein-RNA interface
Amita Barik1, Abhishek Mishra, Ranjit Prasad Bahadur
1Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India.
Nucleic Acids Research
|June 13, 2012
Summary
PRince is a web server for analyzing protein-RNA interactions. It provides structural and physicochemical properties of the interface, aiding in understanding recognition specificity.
Area of Science:
- Structural Biology
- Computational Biology
- Biochemistry
Background:
- Protein-RNA interactions are crucial for numerous biological processes.
- Understanding the molecular basis of these interactions is key to deciphering cellular functions.
- Existing tools may not comprehensively analyze the multifaceted properties of protein-RNA interfaces.
Purpose of the Study:
- To develop a web server, PRince, for detailed analysis of protein-RNA interfaces.
- To provide insights into the structural features and physicochemical properties governing protein-RNA recognition.
Main Methods:
- Users submit protein-RNA complex PDB files and chain identifiers.
- The server calculates interface size via buried solvent accessible surface area.
- It computes structural, physicochemical, and hydration properties of interacting surfaces.
Main Results:
- PRince generates a comprehensive set of parameters characterizing the protein-RNA interface.
- Results are presented in tabular format and can be visualized using Jmol.
- Atomic coordinates of interface molecules and water are downloadable.
Conclusions:
- PRince offers novel parameters to correlate with experimental data for understanding protein-RNA recognition specificity.
- The server is publicly accessible and free, with plans for future upgrades.
Related Concept Videos
02:04Protein-protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
02:04Protein-Protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...