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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...
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 Families02:47

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 locations, protein...
Protein Families02:47

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 locations, protein...
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.
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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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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COMA server for protein distant homology search.

Mindaugas Margelevicius1, Mindaugas Laganeckas, Ceslovas Venclovas

  • 1Institute of Biotechnology, Graiciūno 8, Vilnius, Lithuania.

Bioinformatics (Oxford, England)
|June 10, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a new web server for detecting distant protein homology using sequence profile-profile comparisons. This tool aids in studying protein evolution, structure, and function, and identifies new members of the PD-(D/E)XK nuclease superfamily.

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09:37

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Published on: July 12, 2022

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Distant homology detection is crucial for understanding protein evolution, structure, and function.
  • Existing methods often require significant computational resources or specialized expertise.

Purpose of the Study:

  • To develop and present a user-friendly web server for efficient homology searching.
  • To enable the identification of novel protein relationships and superfamily members.

Main Methods:

  • Implementation of a sequence profile-profile comparison algorithm.
  • Creation of regularly updated profile databases for homology searches.
  • Development of a web server interface for single sequence or multiple sequence alignment inputs.

Main Results:

  • The web server successfully detects distant homologies.
  • New members of the PD-(D/E)XK nuclease superfamily were identified.
  • Profile databases are available for download for local use.

Conclusions:

  • The developed web server provides a valuable resource for computational protein analysis.
  • This approach enhances the study of protein evolution, structure, and function.
  • The tool facilitates the discovery of new protein families and superfamilies.