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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Published on: July 16, 2017

3D-SURFER: software for high-throughput protein surface comparison and analysis.

David La1, Juan Esquivel-Rodríguez, Vishwesh Venkatraman

  • 1Department of Biological Sciences, College of Science, Purdue University, West Lafayette, IN 47907, USA.

Bioinformatics (Oxford, England)
|September 18, 2009
PubMed
Summary
This summary is machine-generated.

3D-SURFER is a new web tool for rapid protein surface shape comparison. It uses 3D Zernike descriptors for fast analysis and visualization of protein structures.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biochemistry

Background:

  • High-throughput screening of protein structures is crucial for understanding biological function.
  • Existing methods for protein comparison can be computationally intensive.
  • Characterizing protein surface shape is key to identifying functional sites.

Purpose of the Study:

  • To develop and present 3D-SURFER, a web-based tool for efficient protein surface shape comparison and characterization.
  • To enable high-throughput analysis of protein structures from the Protein Data Bank (PDB).

Main Methods:

  • Proteins are represented using 3D Zernike descriptors, creating a vector representation of their surface shape.
  • A web interface facilitates interactive visualization, including animated rotations and structural alignments.
  • The CE program is utilized for structural alignments.

Main Results:

  • 3D-SURFER enables rapid comparison of a query protein against the entire PDB in seconds.
  • The tool identifies and visualizes geometrically significant local surface features, such as pockets and protrusions.
  • Interactive displays enhance user experience and data interpretation.

Conclusions:

  • 3D-SURFER provides an efficient and interactive platform for high-throughput protein surface shape analysis.
  • The tool aids in the characterization of proteins and identification of potential ligand-binding sites.
  • Web accessibility and speed make 3D-SURFER a valuable resource for structural biologists.