Name
Abstract | ||
|---|---|---|
For a complex molecular system the delineation of atom-atom contacts, exposed surface and binding sites represents a fundamental step to predict its interaction with solvent, ligands and other molecules. Recently, atom depth has been also considered as an additional structural descriptor to correlate protein structure with folding and functional properties. The distance between an atom and the nearest water molecule or the closest surface dot has been proposed as a measure of the atom depth, but, in both cases, the 3D character of depth is largely lost. In the present study, a new approach is proposed to calculate atom depths in a way that the molecular shape can be taken into account.An algorithm has been developed to calculate intersections between the molecular volume and spheres centered on the atoms whose depth has to be quantified. Many proteins with different size and shape have been chosen to compare the results obtained from distance-based and volume-based depth calculations. From the wealth of experimental data available for hen egg white lysozyme, H/D exchange rates and TEMPOL induced paramagnetic perturbations have been analyzed both in terms of depth indexes and of atom distances to the solvent accessible surface. The algorithm here proposed yields better correlations between experimental data and atom depth, particularly for those atoms which are located near to the protein surface.Instructions to obtain source code and the executable program are available either from http://sienabiografix.com or http://sadic.sourceforge.netniccolai@unisi.ithttp://www.Sienabiogzefix.com/publication. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1093/bioinformatics/bti444 | Bioinformatics |
Keywords | Field | DocType |
solvent accessible surface,protein surface,atom contact,exposed surface,atom depth,experimental data,depth index,closest surface,atom distance,three-dimensional computation,complex molecular structure,volume-based depth calculation,molecular structure,three dimensional,protein structure,binding site | Data mining,Molecular physics,Molecule,Paramagnetism,Computer science,Molecular geometry,Atom,Accessible surface area,SPHERES,Protein structure,Computation | Journal |
Volume | Issue | ISSN |
21 | 12 | 1367-4803 |
Citations | PageRank | References |
5 | 0.59 | 2 |
Authors | ||
8 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Daniele Varrazzo | 1 | 5 | 0.59 |
| Andrea Bernini | 2 | 8 | 3.60 |
| Ottavia Spiga | 3 | 8 | 3.26 |
| Arianna Ciutti | 4 | 5 | 0.59 |
| Stefano Chiellini | 5 | 5 | 0.59 |
| Vincenzo Venditti | 6 | 5 | 0.59 |
| Luisa Bracci | 7 | 5 | 0.59 |
| Neri Niccolai | 8 | 8 | 2.52 |