Home  About  Methodology  Help  Example Run  Citations  Group  Report Bug  Related Tools 
Methodology 
For any given PDB complex; once the chain ids, for which the interactions are to be calculated, are selected; PPCheck calculates the energy values for the above listed nonbonded interactions and sum them up to obtain the total stabilizing energy (E_{t}). Total stabilizing energy is then divided by the total number of interface residues to obtain the energy per residue (E_{nt}) for that complex. Please see the following flowchart for better explanation. 
Figure 1: Flowchart 

E = q_{1}q_{2} [1/r(ON) + 1/r(CH)  1/r(OH)  1/r(CN)] * 332 * 4.184 kJ/mol 



where R is the Van der Waals radius for an atom, E is the van der Waals well depth, r is the distance between the atoms. All interprotomer atomic pairs 7 Å or less apart are considered for energy calculation. The van der Waals interaction also accounts for hydrophobic interactions and shorts contacts (Ramachandran & Sasisekaran, 1968 and Novotny et al., 1997). 

where q1 and q2 are the partial atomic charges, r is the distance between the atoms and D is the dielectric constant of the medium, distance dependent diletric (DDD, where D=2r) is used for the energy calculation. The values for the different parameters are as in CHARMM (Brooks et al., 1983 & Brooks et al., 2009). 

D = r  (R  0.40) where R is the sum of the van der Waals radii of the two atoms and r is the distance between the atoms.If D < 0, the atomic interaction is marked as a short contact as described (Ramachandran et al., 1963 and Lomize et al., 2002). 









