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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.
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The primary structure of a protein is its amino acid sequence.
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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Conservation of Protein Domains02:26

Conservation of Protein Domains

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Related Experiment Video

Updated: May 18, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

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

Published on: August 16, 2017

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.

Noah M Daniels1, Shilpa Nadimpalli, Lenore J Cowen

  • 1Department of Computer Science, Tufts University, 161 College Ave, Medford, MA 02155, USA.

BMC Bioinformatics
|October 9, 2012
PubMed
Summary
This summary is machine-generated.

Formatt enhances protein structure alignment by integrating sequence similarity with geometric data. This novel approach improves alignment quality, outperforming existing methods on benchmark datasets.

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Last Updated: May 18, 2026

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09:37

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Published on: July 12, 2022

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Traditional protein structure alignment relies solely on geometric properties of backbone atoms.
  • Incorporating sequence similarity into structural alignment has been challenging.
  • Existing methods often neglect valuable sequence information.

Purpose of the Study:

  • To develop a novel multiple structure alignment program, Formatt, that integrates sequence similarity.
  • To evaluate Formatt's performance against established geometric and sequence-aware alignment tools.
  • To assess the impact of sequence information on the quality of protein structure alignments.

Main Methods:

  • Formatt builds upon the Matt geometric alignment program.
  • Formatt incorporates sequence similarity measures during alignment construction.
  • Performance was evaluated using HOMSTRAD and SABMark benchmark datasets.

Main Results:

  • Formatt demonstrated superior performance over Matt and other popular programs on the HOMSTRAD benchmark.
  • On the SABMark dataset (remote homology), Formatt and Matt outperformed other methods.
  • Formatt achieved better sequence and structural alignments with a smaller core size, or comparable alignments with improved sequence similarity, compared to Matt.

Conclusions:

  • Integrating sequence information alongside geometric data enhances multiple protein structure alignment quality.
  • Defining optimal alignments when sequence and structural information conflict remains an open research question.
  • Formatt represents a significant advancement in aligning protein structures with evolutionary context.