rules according to CHARMM force field [32]. The input and
output files are in PDB format. As most protein structures in
PDB lack hydrogen atoms, AddH can be used to prepare the
input of Cyscore program.
Website
Cyscore program Package is available at the site:http://clab.
labshare.cn/software/.3 Methods
3.1 Installation Extract the Cyscore.tar.gz and place the folder anywhere in the disk
without modifying the newly built subdirectories and files. Three
subdirectories will appear:
bin: it contains all the executable binary files of this package.
dat: it contains the parameter files.
example: it contains example data files and the readme file.
Users are allowed to run the software in a different directory
by specifying the program path in the command: (<program
path>/bin/Cyscore). The program will find the parameter files
automatically.
Please note, programs in Cyscore package need to be run on
Linux system (seeNote 4).
3.2 Cyscore Program Usage:
Cyscore [input protein PDB file] [input ligand Mol2 file]Cyscore predicts the binding free energy between the query
protein and ligand. It requires protein and ligand containing hydro-
gen atoms. For a protein structures downloaded from Protein Data
Bank (PDB), the hydrogen atoms are suggested adding by AddH in
this package (seeNote 5). As for ligand, the hydrogen atoms could
be added by OpenBabel (http://openbabel.org/wiki/Main_
Page), which is a well-established chemical software for searching
and converting compounds. Cyscore was fitted on experimentally
determined binding affinity data. The score has the dimension of
kcal/mol. Therefore the lower score indicates the higher binding
affinity.
Example:
Open the terminal and change the directory to the installed
subdirectory of “example”. Run:$../bin/Cyscore 3nw9_protein.pdb 3nw9_ligand.mol2Then the output is printed on the screen (Shown in Fig.2).
The first line below the title lists names of input files. The following
line shows energies of hydrophobic term, van der Waals interaction236 Yang Cao et al.