Bioinformatics Vol. 19 no. 2 2003
Pages 313-314
© 2003 Oxford University Press
Applications Note |
DPX: for the analysis of the protein core
1 Protein Structure and Bioinformatics Group, International Center for Genetic Engineering and Biotechnology
(ICGEB), AREA Science Park, Padriciano 99, 34012 Trieste
2 Department of General Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
Received on May 23, 2002
; revised on July 22, 2002
; accepted on September 13, 2002
Summary: 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 (Å) 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.
Availability: 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.
Contact: pintar{at}icgeb.org; carugo{at}icgeb.org; pongor{at}icgeb.org
* To whom correspondence should be addressed.
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