Computational Drug Discovery and Design

atom types helps in determining the parameters to be used for

each atom. If the protein is considered to be static and frag-

ments are treated rigid, only nonbonded parameters are

needed. Generally, for such a procedure, AMBER force field

is used [47]. Performance of AMBER for studying

protein–fragments interactions has already being reported

[48–51].

4.Distribution of charge

This step involves the calculation of point charges of atoms

for all the 3D conformers generated. Gaussian is used to

Fig. 1Graphical depiction of the methodology for structure-based de novo drug

designing

130 Shashank P. Katiyar et al.