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Bioinformatics Vol. 18 no. 7 2002
Pages 980-984
© 2002 Oxford University Press

CX, an algorithm that identifies protruding atoms in proteins

Alessandro Pintar 1,*, Oliviero Carugo 1,2 and Sándor Pongor 1,*

1 Protein Structure and Bioinformatics Group, International Center for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34012 Trieste, Italy
2 Department of General Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy

Received on December 12, 2001 ; revised on February 6, 2002 ; accepted on February 14, 2002

Motivation: A simple and fast algorithm is described that calculates a measure of protrusion (cx) for atoms in protein structures, directly useable with the common molecular graphics programs.

Results: A sphere of predetermined radius is centered around each non-hydrogen atom, and the volume occupied by the protein and the free volume within the sphere (internal and external volumes, respectively) are calculated. Atoms in protruding regions have a high ratio (cx) between the external and the internal volume. The program reads a PDB file, and writes the output in the same format, with cx values in the B factor field. Output structure files can be directly displayed with standard molecular graphics programs like RASMOL, MOLMOL, Swiss-PDB Viewer and colored according to cx values. We show the potential use of this program in the analysis of two protein–protein complexes and in the prediction of limited proteolysis sites in native proteins.

Availability: The algorithm is implemented in a standalone program written in C and its source is freely available at ftp.icgeb.trieste.it/pub/CX or on request from the authors.

Contact: pintar{at}icgeb.trieste.it; carugo{at}icgeb.trieste.it; pongor{at}icgeb.trieste.it

* To whom correspondence should be addressed.


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