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Related Concept Videos

Protein Families02:47

Protein Families

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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...
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Conservation of Protein Domains Over Different Proteins02:26

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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...
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Protein-Protein Interfaces02:04

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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...
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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

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An intuitive graphical webserver for multiple-choice protein sequence search.

Daniel Banky1, Balazs Szalkai2, Vince Grolmusz1

  • 1Protein Information Technology Group, Eotvos University, Pazmany Peter stny. 1/C, H-1117 Budapest, Hungary; Uratim Ltd., H-1118 Budapest, Hungary.

Gene
|February 15, 2014
PubMed
Summary

The Protein Sequence Analysis server simplifies complex sequence searches. It allows users to intuitively select multiple amino acid choices for specific positions, improving protein sequence analysis.

Keywords:
Multiple choice searchProtein sequence analysisRegular expressionsSequence analysis

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Web-based sequence analysis tools are widely used for tasks like sequence searching and alignment.
  • Current tools, including BLAST, often lack intuitive interfaces for complex queries involving specific residue properties at defined positions.
  • User unfamiliarity with regular expression syntax hinders the formation of sophisticated sequence queries on many platforms.

Purpose of the Study:

  • To introduce an intuitive webserver for protein sequence analysis.
  • To enable the formation of multiple-choice queries based on residue properties and positions.
  • To provide an accessible alternative to complex query syntaxes for researchers.

Main Methods:

  • Development of a user-friendly webserver, the Protein Sequence Analysis server.
  • Implementation of a graphical interface for selecting amino acid residues at specific positions.
  • Support for multiple residue choices per position and categorization by physicochemical properties (e.g., hydrophobic, polar).

Main Results:

  • The Protein Sequence Analysis server offers an intuitive, computer-game-like interface for query formation.
  • Users can easily specify multiple amino acid options or residue types (e.g., hydrophobic) for given positions.
  • The server simplifies the creation of complex protein sequence queries that were previously difficult to formulate.

Conclusions:

  • The Protein Sequence Analysis server enhances the accessibility of advanced sequence analysis.
  • Its intuitive design lowers the barrier for researchers to perform complex sequence searches.
  • This tool represents a significant improvement for protein sequence analysis workflows.