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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

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 Organization01:24

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 Sites01:49

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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Conservation of Protein Domains02:26

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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Related Experiment Video

Updated: Jun 16, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: July 14, 2015

Multiple structure alignment and consensus identification for proteins.

Ivaylo Ilinkin1, Jieping Ye, Ravi Janardan

  • 1Department of Computer Science, Gettysburg College, Gettysburg, PA, USA. iilinkin@gettysburg.edu

BMC Bioinformatics
|February 4, 2010
PubMed
Summary
This summary is machine-generated.

A new algorithm aligns multiple protein structures and generates a consensus protein, capturing common substructures. This method is fast, accurate, and comparable to existing tools for protein structure analysis.

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Related Experiment Videos

Last Updated: Jun 16, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: August 16, 2017

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein structure alignment is crucial for understanding protein function and evolution.
  • Existing methods often face challenges in speed and accuracy for multiple protein alignments.
  • Developing efficient algorithms for multiple protein structure alignment is an ongoing research area.

Purpose of the Study:

  • To present a novel algorithm for multiple protein structure alignment.
  • To generate a consensus (pseudo) protein representing common structural features.
  • To provide a computationally efficient tool for structural bioinformatics.

Main Methods:

  • Representing proteins as sequences of alpha-carbon coordinate triples.
  • Iteratively computing transformation matrices (translations and rotations) for alignment.
  • Employing a heuristic approach to approximate optimal alignment by minimizing pairwise distances.

Main Results:

  • The algorithm demonstrates rapid convergence and produces visually similar consensus structures.
  • It is competitive with established algorithms like MAMMOTH and MATT in speed and discovery of conserved regions.
  • The algorithm has been implemented in C++ and is accessible via a web server.

Conclusions:

  • The presented algorithm effectively computes multiple protein structure alignments and generates consensus structures.
  • Experimental results validate its effectiveness in terms of alignment quality and computational efficiency.
  • The tool is readily available for use in protein structure analysis.