CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures.
The WWW servers at http://www.icgeb.org/protein/ are dedicated to the analysis of protein 3D structures submitted by the users as the Protein Data Bank (PDB) files. CX computes an atomic protrusion index that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index for the buried atoms and makes it possible to analyze the distribution of buried residues. CX and DPX return PDB files containing the calculated indices that can then be visualized using standard programs, such as Swiss-PDBviewer and Rasmol. PRIDE compares 3D structures using a fast algorithm based on the distribution of inter-atomic distances. The options include pairwise as well as multiple comparisons, and fold recognition based on searching the CATH fold database.
Vlahovicek
Kristian
K
Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy.
Pintar
Alessandro
A
Parthasarathi
Laavanya
L
Carugo
Oliviero
O
Pongor
Sándor
S
D000465:Algorithms; D003196:Computer Graphics; D020407:Internet; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D012984:Software
D011506:Proteins