CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C Citation C C Shijun Zhong and Alexander D. MacKerell, C C Binding Response: A Descriptor for Selecting Ligand Binding Site C C on Protein Surfaces. J. Chem. Inf. Model. 2007, 47(6), 2303-2315. C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
I. INTRODUCTION II. DOWNLOAD III. INSTALLATION IV. COMPUTATION 1. The primary level Input Output 2. The extended level Input Output 3. User's computation
Binding Response (BR) is a method to select ligand binding sites on protein surfaces for virtual database screening. The binding response values are designed to be in the range [0, 1]. A good binding site should receive a relatively large binding response value. See original manuscript for more details.
Evaluation of the binding response value requires calculation of the binding energy and the geometrical pose for a set of probe ligands docked against the concerned binding site. Therefore, a test docking of a set of small molecules needs to be performed in advance. Currently, the software DOCK is used to generate the binding poses and energy scores which are recorded in the *.mol2 format recongnizable to the present program.
The current package provides three options to perform the calculations. The first, partial option is the calculation of the binding response values for a binding site based on previously generated docking results. The second, extended option is a complete procedure for identifying binding sites starting from generating the protein surface and expressing the binding pockets, through docking, and ending with the ranking of binding sites. The remainder of this document describes the implementation of options 1 and 2. The third option is an alternate collection of scripts to perform the complete binding response calculations by Kenno Vanommeslaeghe; see bindres.html in the bindres subdirectory.
Please email alex@outerbanks.umaryland.edu and request the package "binding_response.tar.gz". Use the following command to extract this gzipped file.
tar -xvzf binding_response.tar.gzA directory "binding_response" will be automatically generated. It contains the following files and directories.
README.html this file bin directory of executable files: br.exe and some scripts src directory of the source code examples directory of examples for running br.exe demo directory for demo calculation for the second, extended option parameter directory of parameter files and input files test work directory for performing the individual user's calculations user_modified directory for future user scripts bindres directory containing alternate scripts for calculation of the binding response
All executable files in the package were tested in a Linux environment and are ready for running the first, partial option. The source code is included in the src directory.
The calculation for the second, extended options requires a series of calculations using other programs, i.e. CHARMM, DMS, and DOCK. These programs should be installed in advance to generate the following executable files:
charmm, dms, sphgen, showbox, grid, dock.Copy these files to the directory "binding_response/bin" so that it does not need to change the path defined in the script file "binding_response/bin/br.csh".
No parameter file is required for the CHARMM calculation. However, the docking calculation needs the DOCK parameter files:
chem.defn, flex.defn, flex_drive.tbl, vdw_AMBER_parm99.defnCopy them to the subdirectory "binding_response/parameter" so that it is not necessary to change the path defined in the DOCK4.0 input files "grid.in" and "dock.in" which can be modified to fit user's DOCK version.
1. First option
The following example describes how to compute the binding response value for a binding site.
cd binding_response/examples ../bin/br.exe < ex1.inp > ex1.out
Input
The input file "ex1.inp" requires only two file names in separate lines, i.e.
ex1.mol2 ex1.sphex1.mol2 is a previously generated DOCK mol2 file which contains the energy score and the coordinates of the ligands previously docked to the binding site. It is suggested that the summation of electrostatic and van del Waals interactions be used as the energy score in the docking. Currently, the mol2 files generated by DOCK4, DOCK5, and DOCK6 can be recognized by the program.
ex1.sph, in the format of the SPHGEN output, contains a set of spheres which defines the effective space of the binding pocket. It should be pointed out that the sphere set can be different from that used in docking.
Output
The output gives the averaged binding response (BR) values for the first 10 compounds, for the first 100 compounds, ..., and for all compounds.
Ligand_N E_aver BR 10 -34.4760 0.9985 100 -28.7006 0.9729 108 -27.9581 0.9663
For example, the Binding Response value is 0.9663 for the binding site defined by the sphere set (ex1.sph) for the 108 docked compounds (ex1.mol2).
2. Second, extended optin
The following demo calculation shows the entire procedure of ranking binding sites on protein surfaces.
cd binding_response/demo ./demo.csh &
Input
The executable file "demo.csh" will automatically read two protein structure files
protein.pdb protein.mol2which exist in the current directory.
"protein.pdb" contains no hydrogen atoms and will be called by the program "SPHGEN" to generate the protein surface.
"protein.mol2" will be used in docking and therefore contains hydrogen atoms and atomic partial charges.
Output
The output file "br.out" will include:
The top 10 binding sites evaluated based on the binding energy and pose of 2 ligands docked against each of these binding sites. Preferred binding sites will have a larger BR value as given in the last column of the following table. Binding_Site Spheres E_averaged BR(all_ligands) pdbid_clust_6 16 -27.3750 0.9672 pdbid_clust_9 16 -24.7800 0.9298 pdbid_clust_8 22 -20.5750 0.9292 pdbid_clust_2 26 -20.3750 0.9288 pdbid_clust_5 16 -18.7650 0.9120 pdbid_clust_1 25 -23.8150 0.8959 pdbid_clust_7 16 -19.5150 0.8686 pdbid_clust_4 15 -20.1800 0.7701 pdbid_clust_3 17 -20.5150 0.7621 pdbid_clust_10 14 -16.4300 0.5309
Thus, the binding site labelled "pdbid_clust_6" is highest ranked binding site with the largeest Binding Response value: 0.9672.
3. User's computation
For application of the method on alternate proteins
cd binding_response/testCopy your protein pdb and mol2 files to the current directory and rename them to:
protein.pdb protein.mol2Type the command:
../bin/br.csh &It takes about 60 hours of CPU time on an 2GHz 64bit AMD Athlon with 1GB of memory to complete the full calculation, including all docking. Then check the output file "br.out" for the results.