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Related Experiment Videos

PROFbval: predict flexible and rigid residues in proteins.

Avner Schlessinger1, Guy Yachdav, Burkhard Rost

  • 1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. profbval@rostlab.org

Bioinformatics (Oxford, England)
|February 4, 2006
PubMed
Summary

We developed PROFbval, a novel web server that predicts protein residue flexibility from amino acid sequence. This tool aids in identifying functionally important residues by analyzing B-value data, crucial for protein function studies.

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Area of Science:

  • Protein bioinformatics
  • Structural biology
  • Computational biology

Background:

  • Protein surface residue mobility is intrinsically linked to protein function.
  • Identifying rigid or flexible residues is key to understanding functionally important sites.
  • B-value data from X-ray structures typically measures protein mobility.

Purpose of the Study:

  • To present PROFbval, the first web server for predicting normalized B-values directly from amino acid sequence.
  • To provide a tool for identifying functionally important residues based on predicted mobility.
  • To offer predictions of both normalized B-values and two-state flexibility/rigidity.

Main Methods:

  • Development of the PROFbval web server.
  • Input accepts amino acid sequences or alignments.

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  • Output includes normalized B-value predictions and two-state flexibility/rigidity assignments.

    • Main Results:

    • PROFbval accurately predicts normalized B-values from sequence.
    • The server provides a reliability index for each prediction.
    • Demonstrated ability to identify rigid residues in enzyme active sites.

    Conclusions:

    • PROFbval offers a novel method for predicting protein residue mobility from sequence data.
    • The tool facilitates the identification of functionally significant residues.
    • This approach enhances the understanding of protein structure-function relationships.