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Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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.

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 analyses the...

Conservation of Protein Domains

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

Protein and Protein Structures

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Related Experiment Video

Updated: May 29, 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

Optimizing a widely used protein structure alignment measure in expected polynomial time.

Aleksandar Poleksic¹

¹Department of Computer Science, University of Northern Iowa, 305 ITTC, Cedar Falls, IA 50614-0507, USA. poleksic@cs.uni.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|September 10, 2011

Summary

This study analyzes protein structure similarity using atom superposition. Researchers proved a recently developed algorithm for this measure runs in polynomial time, improving computational biology tools.

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Last Updated: May 29, 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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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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:

Computational molecular biology
Bioinformatics
Structural biology

Background:

Protein structure alignment is crucial for biological applications like evolution studies, modeling, and drug design.
The complexity arises from the vast number of possible spatial orientations between protein structures.
Assessing pairwise protein structure similarity is a key challenge.

Purpose of the Study:

To analyze a common measure of pairwise protein structure similarity.
To evaluate the computational efficiency of a recently published algorithm for optimizing this similarity measure.

Main Methods:

The study focuses on a similarity measure based on the number of superimposable atom pairs within a distance cutoff.
Theoretical analysis was used to determine the algorithm's running time complexity.

Main Results:

The expected running time of the analyzed algorithm was proven to be polynomial.
This finding addresses the computational challenge in protein structure alignment.

Conclusions:

The algorithm provides an efficient method for calculating protein structure similarity.
This advancement supports applications in protein evolution, modeling, and drug design.