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

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

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

  1. 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.