2.7 Molecular docking
In order to predict the possible interaction patterns between natural
compounds and STAT3, molecular docking studies were carried out using
Autodock 4.2 software (The Scripps Research Institute, La Jolla, CA,
USA). The preparations related to Autodock docking were performed using
the Autodock Tools (ADT). The three-dimensional (3D) crystal structure
of STAT3 (PDB code: 1BG1) was retrieved from the RCSB Protein Data Bank
(PDB; http://www.rcsb.org/pdb/). The standard 3D structures of natural
compounds were constructed by using the “SKETCH” option function in
SYBYL-X 2.1 (Tripos International, St. Louis, MO, USA). The Lamarckian
genetic algorithm (LGA) was used to implement the molecular docking. The
docking parameters were set as follows: population size, 150; number of
generations, 270 000; number of evaluations, 25 000 000; number of top
individuals that automatically survive, 20; and number of docking runs,
40. The default values of the remaining parameters were used.