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CX, an algorithm that identifies protruding atoms in proteins.

Alessandro Pintar1, Oliviero Carugo, Sándor Pongor

  • 1Protein Structure and Bioinformatics Group, International Center for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34012 Trieste, Italy. pintar@icgeb.trieste.it

Bioinformatics (Oxford, England)
|July 16, 2002
PubMed
Summary

A new algorithm quantifies atom protrusion (cx) in protein structures. This method, implemented in a C program, aids in analyzing protein complexes and predicting proteolysis sites.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Assessing atomic protrusion is crucial for understanding protein structure and function.
  • Existing methods may lack speed or direct integration with visualization tools.

Purpose of the Study:

  • To introduce a simple, fast algorithm for calculating atomic protrusion (cx) in protein structures.
  • To provide a tool directly usable with common molecular graphics programs.

Main Methods:

  • A C-based program calculates the ratio of external to internal free volume around each non-hydrogen atom.
  • The protrusion index (cx) is determined by comparing occupied and free volumes within a defined sphere.
  • Output cx values are integrated into PDB files' B-factor fields for visualization.

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Main Results:

  • The algorithm efficiently calculates atomic protrusion (cx) for protein structures.
  • Protrusion values (cx) can be visualized using standard molecular graphics software (e.g., RASMOL, MOLMOL).
  • The method demonstrates utility in analyzing protein-protein complexes and predicting proteolysis sites.

Conclusions:

  • The developed algorithm and program provide a valuable tool for structural analysis.
  • Its direct integration with visualization software enhances the study of protein surfaces.
  • The method shows promise for applications in protein-protein interactions and stability studies.