term, hydrogen-bond term, and the ligand’s entropy loss term. The
first three terms are usually negative. Only if there are strong atomic
clashes between the protein and ligand, van der Waals interaction
term is positive. If the ligand is not docked on the protein, the first
three terms is zero. Cyscore on the last line is the summation of
above terms.3.3 Curvature-
Surface Program
Usage:CurvatureSurface [input PDB file or Mol2 file] [output PDB file
for solvent accessible surface grid]CurvatureSurface supports PDB or SYBYL MOL2 format
input files. The output file can be visualized by molecular visualiza-
tion software such as Pymol or RasMol. The detailed information of
surface grid, can be browsed by a text editor, such as gedit or vim.
Figure3 illustrates the format of output file. The first line is the
remark information such as the creating time and program name of
the file. The following ATOM records indicate the index of grid
points (2nd column), grid type name (3rd column), grid name (4th
column), the index of molecular atoms which form the surface grid
(5th column), three-dimensional coordinates (6–8th column), and
the curvature data (10th column, highlight in red) of the grid
points. The curvature data varies from 1 to 20. The curvature
data larger than 10 implies that the grid point is at concave region.
Example:
Open the terminal and change the directory to the installed
subdirectory of “example”. Run:$ ../bin/CurvatureSurface 3nw9_protein.pdb 3nw9_protein_grid.
pdbThe program will generate a new file named 3nw9_protein_-
grid.pdb. It can be opened by Pymol, RasMol, or other molecular
visualization software. Figure4a and 4b demonstrate the visualiza-
tion of grid by Pymol and RasMol respectively. The grid is colored
by b-factor or temperature. The warm color region highlights
concave surface which could be the binding pocket. The largestFig. 2The output of Cyscore prediction
Protein-Ligand Docking by Cyscore 237