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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.
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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

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Updated: Jun 1, 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

iPBA: a tool for protein structure comparison using sequence alignment strategies.

Jean-Christophe Gelly¹, Agnel Praveen Joseph, Narayanaswamy Srinivasan

¹INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Université Paris Diderot-Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France.

Nucleic Acids Research

|May 19, 2011

Summary

This summary is machine-generated.

We developed iPBA, a fast and efficient protein structure comparison tool using a structural alphabet. iPBA significantly improves alignment accuracy and outperforms existing methods for both pairwise and database searches.

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Area of Science:

Structural bioinformatics
Computational biology
Protein structure analysis

Background:

The rapid increase in protein structure data necessitates efficient comparison methods.
Protein Blocks (PBs) offer a way to represent 3D protein structures as 1D sequences.

Purpose of the Study:

To present the iPBA web server, an improved method for protein structure comparison.
To enhance the accuracy and efficiency of protein structure alignments.

Main Methods:

Utilizing a structural alphabet (Protein Blocks) to convert 3D protein structures into 1D sequences.
Implementing an improved alignment approach with specialized PB Substitution Matrices (SM) and anchor-based methodology.
Developing a web server for pairwise comparisons and database searches, including local alignment for sub-structural similarity.

Main Results:

The iPBA method, using specialized SM and anchor-based alignment, improved the quality of approximately 88% of alignments.
iPBA alignments demonstrated superior performance compared to DALI, MUSTANG, and GANGSTA(+) in over 80% of cases.
The web server provides sequence alignments and superposed 3D structures visualized with PyMol and Jmol.

Conclusions:

iPBA provides a fast, efficient, and accurate method for protein structure comparison.
The tool is valuable for detecting both global and sub-structural similarities.
iPBA is a significant contribution to the scientific community for analyzing protein structures.