CX, an algorithm that identifies protruding atoms in proteins.
BACKGROUND
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.


BACKGROUND
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.
Pintar
Alessandro
A
Protein Structure and Bioinformatics Group, International Center for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34012 Trieste, Italy. pintar@icgeb.trieste.it
Carugo
Oliviero
O
Pongor
Sándor
S
D000465:Algorithms; D003196:Computer Graphics; D030562:Databases, Protein; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D011381:Programming Languages; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D012680:Sensitivity and Specificity; D015843:Serpins / Q000737:chemistry; D012984:Software; D014357:Trypsin / Q000737:chemistry
D011506:Proteins; D015843:Serpins; D014357:Trypsin