## 4 Models and Methods
### DynDom and Surface Analyses  
DynDom is able to determine dynamic domains, hinge axes, and hinge-bending residues from two protein structures that have different conformations. DynDom generates short segments of the amino-acid chains of these proteins by use of a sliding window and the calculation of the rotation vector associated with the rotation of these segments between the two structures. By treating the components of these rotation vectors as coordinates in a \"rotation space\", segments that rotate together will have rotation points collocated, indicating possible rigid domains within the structure. Moreover, in creating a domain decomposition, DynDom measures the ratio of interdomain displacement to intradomain displacement as defined by [PERSON] & Berendsen [68]. For a domain decomposition to beaccepted for the hinge axis analysis, this ratio must be larger than 1.0, _i.e.,_ there must be more interdomain displacement than intradomain displacement. Thus, domains can be identified from the distribution of rotation points. Domains and hinge axes were identified and characterized by using the DYNDOM program ([[http://www.cmp.uea.ac.uk/dydndom/](http://www.cmp.uea.ac.uk/dydndom/)]([http://www.cmp.uea.ac.uk/dydndom/](http://www.cmp.uea.ac.uk/dydndom/))).  
Shape descriptors representing protein structure, such as depth, surface curvature, extreme elevation, surface area and volume, have been used extensively to identify, study and compare protein ligand interactions, protein-protein interactions and the respective binding sites. We have used CASTp server to determine the binding pocket ([[http://sts.bioengr.uic.edu/castp/](http://sts.bioengr.uic.edu/castp/)]([http://sts.bioengr.uic.edu/castp/](http://sts.bioengr.uic.edu/castp/))) [69]. CASTp server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules. It measures analytically the area (in A\({}^{2}\)) and volume (in A\({}^{3}\)) of each pocket and cavity, both in solvent accessible surface (SA, Richards' surface) and molecular surface (MS, Connolly's surface) [69]. We set probe radius of 1.4 A as default value. The detected pockets from these algorithms ranked with their volumes and areas. For ligand molecules internal protein cavities appear to be a favored binding site, and the cavity volume may play an important role in the strength of the guest molecule-host cavity interaction. In CASTp analysis, we have chosen the platinum-binding pockets for our analysis.  
To analyze the influence of electrostatic properties on biochemical system, the PDB2 PQR Server ([[http://nbcr-222.ucsd.edu/pdb2](http://nbcr-222.ucsd.edu/pdb2) pqr_1.8/]([http://nbcr-222.ucsd.edu/pdb2](http://nbcr-222.ucsd.edu/pdb2) pqr_1.8/)) was employed to convert the protein files in PDB format to PQR format in which the occupancy and B-factor columns have been replaced by per-atom charge and radius [70,71]. The Pymol molecular graphics software package provides support for both the evaluation of the electrostatic properties and the visualization of the resulting electrostatic potentials with PQR file.