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Related Concept Videos

Protein Families02:47

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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 locations, protein...
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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CFP: a web-server for constructing sequence-based protein conformational flexibility profiles.

Igor B Kuznetsov1, Shalom Rackovsky

  • 1Cancer Research Center, Department of Epidemiology and Biostatistics, University at Albany, One Discovery Drive, Rensselaer, NY 12144, USA. ikuznetsov@uamail.albany.edu

Bioinformation
|May 13, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces the Conformational Flexibility Profile (CFP) web server, which predicts protein backbone flexibility using the generalized local propensity (GLP) measure. It helps identify flexible protein segments and assess their statistical significance.

Keywords:
conformational variabilityflexibilitylocal propensityprotein backbonesequence

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Proteins often feature flexible segments with dynamic backbone conformations.
  • Predicting protein flexibility is crucial for understanding protein function and dynamics.

Purpose of the Study:

  • To present the Conformational Flexibility Profile (CFP) web server.
  • To enable identification of protein backbone flexible segments using sequence data.

Main Methods:

  • Developed the generalized local propensity (GLP) as a quantitative, sequence-based measure of protein backbone flexibility.
  • Implemented the CFP web server to generate GLP flexibility profiles from user-submitted sequences.
  • Utilized discrete scan statistics to assess the significance of identified flexible segments based on residue density.

Main Results:

  • The CFP web server successfully constructs GLP flexibility profiles for protein sequences.
  • The server identifies segments exhibiting high backbone flexibility.
  • Statistical assessment of flexible segment significance is provided.

Conclusions:

  • The CFP web server is a valuable tool for analyzing protein conformational flexibility.
  • This approach aids in understanding the functional implications of intrinsically disordered or flexible protein regions.