130 A Practical Guide to Cancer Systems Biology
In essence, it accepts a protein structure file, a compound structure file, and
some other options (such as binding site location) as input, running docking
simulation with an optimization algorithm called Iterated Local Search
global optimizer,^4 then produce a list of binding poses and corresponding
score. However, due to its design, one should use a controller script or
application to input ligand-protein target pairs to Autodock Vina for virtual
screening.
In this chapter, we will introduce the process of running docking (Fig. 1)
from scratch and guide you through the whole process, including fetching and
preparing those structure files and databases, feeding them into Autodock
Vina. Additionally, we will also guide you through the using of SwissDock,^5
a fully automatic docking system.
Figure 1. Overall flowchart of docking simulation. First, structure of the ligand and
the protein target should be fetched from the respected databases. Second, the structures
should be inspected and modified, if necessary, to be able to be used by docking simulation
engine. After the preparations are done, the docking pose(s) can be generated by the
docking simulation application.