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Related Concept Videos

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...
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...

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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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PROCAIN server for remote protein sequence similarity search.

Yong Wang1, Ruslan I Sadreyev, Nick V Grishin

  • 1Biomedical Engineering Program, University of Texas Southwestern Medical Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

Bioinformatics (Oxford, England)
|June 6, 2009
PubMed
Summary
This summary is machine-generated.

PROCAIN is a new web server for detecting distant protein homology using sequence profile comparison. It enhances protein structure and function studies by analyzing multiple signals for accurate homology detection.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Detecting distant protein homology is crucial for understanding protein structure, function, and evolution.
  • Existing methods face challenges in accurately identifying distantly related proteins.
  • PROCAIN was developed to address these limitations.

Purpose of the Study:

  • To introduce the PROCAIN web server for sensitive and accurate detection of distant protein homology.
  • To provide a user-friendly platform for homology searches using sequence profiles.
  • To facilitate research in protein structure, function, and evolution.

Main Methods:

  • PROCAIN employs sequence profile comparison, analyzing residue content similarities.
  • It integrates four signals: profile position similarities, sequence motifs, residue conservation, and predicted secondary structure.
  • The method utilizes a web server for user submissions (query sequence or MSA) and searches against a profile database.

Main Results:

  • The PROCAIN web server enables users to perform homology searches with adjustable input processing and output formatting.
  • Search settings can be customized, including the relative weights of assisting information.
  • The output is presented similarly to BLAST, with homologs sorted by E-value and detailed profile-profile alignments.

Conclusions:

  • PROCAIN offers a robust and versatile tool for identifying distant protein homologs.
  • The web server enhances accessibility for researchers studying protein relationships.
  • This method contributes to advancing the understanding of protein structure, function, and evolutionary pathways.