Computational Drug Discovery and Design

ligand, such as a computationally modeled structure or an apo

structure, the user can provide a potential bound ligand from a

homologous protein structure found in the PDB database (see

Note 1) or provide a center position of the putative binding pocket

identified by a ligand binding site prediction program, such as

VisGrid [26](seeNote 1).

After splitting the receptor and the ligand into separate PDB

files, the SSIC file of the receptor is generated by runningprepar-

e_receptor.pyin thescriptsdirectory:

python prepare_receptor.py [Input file]

An example of the input file is shown below (rec_prep.inin the

exampledirectory):

PLPS_path ~/project/PL-PatchSurfer2/

PDB2PQR_path ~/apps/pdb2pqr

APBS_path /apps/apbs/apbs-1.4/bin

BABEL_path /usr/bin

receptor_file rec.pdb

ligand_file xtal-lig.pdb

The top line,PLPS_path, shows the path of PL-PatchSurfer2 is

installed. Similarly, following three lines designate the locations of

programs. They can be changed to match the user’s environment.

The last two lines,receptor_fileandligand_fileare file names of the

receptor and its cognate ligand.

The output of this script is an SSIC format file named after the

input structure file. For example, if the PDB file’s name isrec.pdb,

then the output is named asrec.ssic. This file contains information

of patches: the coordinates of the patch center, 3DZDs of chemical

features (shape, electrostatic potential, hydrogen bonding, and

hydrophobicity), and the distribution of geodesic distance of

patches. An example of SSIC file is given below:

68 72 144 144 144
5.632 10.269 10.834
0 72 0.16617 0.00000 0.26899 0.27014 0.01290 0.01691 0.20478 0.21539 0.21553
0.04274...
3 144 0.04947 0.00000 0.07677 0.07714 0.00725 0.00944 0.05392 0.05716 0.05732
0.02009...
5 144 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000...
6 144 0.00337 0.00000 0.00726 0.00726 0.00004 0.00006 0.01014 0.01017 0.01017
0.00022...
68012108135513814171721201522212523242024242826213028
27 28 32 30 27 30 37 31 35 29 28 31 27 26 32 24 21 20 22 22 17 24 27 23 22 19 25 18
17 24 27 16 13 16 12 11 13 17 18 21

Virtual Screening with PL-PatchSurfer2 111