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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

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Conserved Binding Sites

Conserved Binding Sites

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Related Experiment Video

Updated: Apr 11, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

UniAlign: protein structure alignment meets evolution.

Chunyu Zhao¹, Ahmet Sacan¹

¹Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA.

Bioinformatics (Oxford, England)

|June 11, 2015

Summary

This summary is machine-generated.

UniAlign improves protein structure alignment by integrating evolutionary data, outperforming existing methods for distantly related proteins. This novel approach enhances the detection of functional residue correspondences.

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Last Updated: Apr 11, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Published on: July 14, 2015

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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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

Area of Science:

Structural bioinformatics
Computational biology
Evolutionary biology

Background:

Protein structure alignment is crucial for understanding protein function and evolution.
Existing methods rely on 3D geometric similarity, limiting detection of functional correspondences, especially for distantly related homologous proteins.
Evolutionary information, such as sequence similarity and residue conservation, is vital for robust alignment.

Purpose of the Study:

To develop a novel protein pairwise structure alignment algorithm (UniAlign) that incorporates evolutionary information.
To improve the detection of functionally relevant residue correspondences between proteins.
To outperform existing structure alignment methods, particularly for distantly related homologous proteins.

Main Methods:

UniAlign algorithm integrates sequence similarity, sequence profiles, and residue conservation.
A per-residue score (UniScore) is defined as a weighted sum of features.
An iterative optimization procedure is employed to find the optimal alignment based on UniScore.
The algorithm is implemented as a web service.

Main Results:

UniAlign demonstrates superior performance compared to commonly used structure alignment methods on benchmark datasets (CDD, HOMSTRAD, BAliBASE).
The algorithm effectively identifies functionally relevant residue correspondences, even for distantly related proteins.
Development of family-specific models further enhances alignment quality.

Conclusions:

UniAlign offers a significant advancement in protein structure alignment by incorporating evolutionary information.
The method enhances the ability to detect functional relationships between proteins.
UniAlign provides a valuable tool for structural bioinformatics and evolutionary studies.