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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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...
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.
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Related Experiment Video

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

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Published on: July 16, 2017

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.

Jan Kosinski1, Alessandro Barbato, Anna Tramontano

  • 1Department of Physics, Sapienza University, 00185 Rome, Italy.

Bioinformatics (Oxford, England)
|February 12, 2013
PubMed
Summary
This summary is machine-generated.

MODexplorer is a tool for exploring protein family diversity, aiding in homology modeling and analysis. It provides sequence, structural, and functional annotations for proteins and their homologs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein family analysis is crucial for understanding biological function.
  • Homology modeling requires accurate sequence and structural information.

Purpose of the Study:

  • To introduce MODexplorer, an integrated tool for exploring protein sequence, structural, and functional diversity.
  • To facilitate homology modeling and general protein family analysis.

Main Methods:

  • Input protein sequence or structure for analysis.
  • Generate alignments with homologs.
  • Provide interactive structural and functional annotations.

Main Results:

  • Offers annotations including sequence conservation, similarity scores, binding sites, secondary structure, disorder, and model quality.
  • Enables analysis of sequence and structural conservation across protein homologs.
  • Facilitates identification of homologs in different conformational states or with varying ligands.

Conclusions:

  • MODexplorer is a valuable resource for analyzing protein families and supporting homology modeling.
  • The tool aids in transferring functional annotations and selecting modeling templates.
  • It assists in building comparative models by leveraging comprehensive annotation data.