DPX: for the analysis of the protein core.
CONCLUSIONS
In order to obtain an accurate description of the protein interior, we describe a simple and fast algorithm that measures the depth of each atom in a protein (dpx), defined as its distance (A) from the closest solvent accessible atom. The program reads a PDB file containing the atomic solvent accessibility in the B-factor field, and writes a file in the same format, where the B-factor field now contains the dpx value. Output structure files can be thus directly displayed with molecular graphics programs like RASMOL, MOLMOL, Swiss-PDB View and colored according to dpx values.


BACKGROUND
The algorithm is implemented in a standalone program written in C and its source is freely available at ftp.icgeb.trieste.it/pub/DPX or on request from the authors.
Pintar
Alessandro
A
Protein Structure and Bioinformatics Group, International Center for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34012 Trieste, Italy. pintar@icgeb.org
Carugo
Oliviero
O
Pongor
Sándor
S
D000465:Algorithms; D003461:Crystallography / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D000077190:Interferon alpha-2; D016898:Interferon-alpha / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011994:Recombinant Proteins; D012984:Software
D000077190:Interferon alpha-2; D016898:Interferon-alpha; D011506:Proteins; D011994:Recombinant Proteins