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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...

Conservation of Protein Domains

Conservation of Protein Domains

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...

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 Families

Protein Families

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...

Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

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Related Experiment Video

Updated: Apr 23, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

PHI-DAC: protein homology database through dihedral angle conservation.

Noa Maatuk¹, Yitav Glantz-Gashai¹, Maya Rotman¹

¹Faculty of Medicine in the Galilee, Bar Ilan University, 13100 Safed, Israel.

Bioinformatics (Oxford, England)

|September 26, 2014

Summary

Scientists can now quickly find similar protein structures using a new database. This tool encodes protein data into text, enabling fast searches for protein segment homologs and evolutionary relationships.

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Last Updated: Apr 23, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

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Published on: January 26, 2024

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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

Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Identifying homologous protein conformations in the Protein Data Bank is crucial for various bioscience disciplines.
Existing methods may lack the speed and interactivity required for efficient exploration of conformational databases.

Purpose of the Study:

To develop a novel database and search engine for identifying protein segment homologs based on dihedral angles.
To facilitate the discovery of conformational similarities and evolutionary relationships among proteins.

Main Methods:

Encoding protein structural information (amino acid sequence, φ and ψ dihedral angles) into text characters.
Implementing a high-speed, interactive search engine for querying the database.

Main Results:

The developed search engine demonstrates high speed, with query times typically lasting only a few seconds.
The system effectively encodes protein coordinates for efficient similarity searching.

Conclusions:

The dihedral angle database and search engine offer a fast and interactive solution for finding protein conformation homologs.
This tool is expected to significantly aid scientists in exploring protein structures and evolutionary connections.