pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes

Immunome Research

Table 2 Comparison of computational time of pDOCK with our earlier docking method

Previous method	pDOCK
Step 1: ~ 5 min
Step 2: ~ 30 s	Preparatory Step 1: ~ 3*s
Step 3: ~ 18 min	Preparatory Step 2: ~ 42.6 s
Step 4^#: ~ 1 min	Single docking and refinement step: ~ 9.24 min
Total: ~ 23.50 – 24.50 *min*	Total: ~ 10 *min*

Both methodologies were applied using a 2 CPU 3.20 GHz 3 GB RAM workstation. *Only for X-ray crystal structures of MHC proteins. The time taken for this step would increase if homology modeling needs to be carried out. ^#Applicable only to MHC-II related peptides.