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Related Concept Videos

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.
Protein and Protein Structures02:15

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...
Protein and Protein Structure02:15

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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Updated: May 9, 2026

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

DoSA: Database of Structural Alignments.

Swapnil Mahajan1, Garima Agarwal, Mohammed Iftekhar

  • 1Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR-S INSERM S665, Faculté des Sciences et Technologies, Université de La Réunion, F-97715 Saint Denis Messag Cedex 09, La Réunion, France.

Database : the Journal of Biological Databases and Curation
|July 13, 2013
PubMed
Summary
This summary is machine-generated.

The Database of Structural Alignments (DoSA) improves protein structure analysis by identifying structurally variable regions (SVRs) often missed in global alignments. It aids in understanding protein function and modeling loop regions.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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Last Updated: May 9, 2026

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

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • * Structural biology
  • * Bioinformatics
  • * Computational biology

Background:

  • * Protein structure alignment is vital for understanding protein function.
  • * Global alignment methods can misclassify structurally similar regions as variable.
  • * Structurally Variable Regions (SVRs) present challenges due to differing spatial orientations.

Purpose of the Study:

  • * To introduce the Database of Structural Alignments (DoSA) for improved identification of local structural similarities.
  • * To address the misclassification of conformationally similar regions as SVRs in global alignments.
  • * To provide a resource for analyzing SVRs and their potential role in protein function.

Main Methods:

  • * Developed a novel algorithm based on protein blocks (a structural alphabet of 16 local motifs) for SVR realignment.
  • * Created the DoSA database containing realignment information for SVRs from pairwise structural alignments of homologous proteins.
  • * Analyzed 74,705 pairwise alignments, identifying 159,780 conformationally similar and 56,140 dissimilar SVRs.

Main Results:

  • * DoSA successfully identifies local structural similarities within SVRs that are obscured in global alignments.
  • * The database provides comprehensive data on conformationally similar and dissimilar SVRs.
  • * Findings highlight the potential of SVR analysis for protein loop modeling and functional studies.

Conclusions:

  • * DoSA enhances the accuracy of protein structure comparison by focusing on SVRs.
  • * The database serves as a valuable resource for researchers studying protein structure-function relationships.
  • * Identified SVRs, particularly those with conserved residues, may be key to the functional integrity of homologous proteins.