Introduction

Thank you very much for purchasing CONFLEX DOCK.
CONFLEX DOCK is a docking simulation program that predicts where a specified peptide chain will coordinate with a substrate protein to form a complex.
When making predictions, the amino acid residues of the protein are coarse-grained at representative points (Cα atoms) and a tetrahedron is constructed by Delaunay partitioning. Then, peptide residues are placed at search points set on the protein surface, and scores are evaluated based on the tetrahedral coarse-grained potentials.

Citation

When publishing calculation results obtained with CONFLEX DOCK in a paper or other publication, please cite the following references
T. Yamamoto, Y. Ikabata, H. Goto, “Reconstruction of Four-Body Statistical Pseudopotential for Protein-Peptide Docking”, J. Comput. Chem., Jpn.-Int. Ed., 2024, 10, 2023-0039.

Execution procedure

The calculation is performed from the command line and the options are as follows.

This section shows how to enter CONFLEX DOCK when it is run from a command.
First, the folders containing the executable files and license parameter files for Windows, macOS, and Linux, respectively, should be as follows

OS	executable file	License Parameters
Windows	C:\CONFLEX\bin	C:\CONFLEX\par
macOS	/Applications/CONFLEX/bin	/Applications/CONFLEX/par
Linux	/usr/local/conflex/bin	/usr/local/conflex/par

To run the calculation with the command, the executable file, the folder of license parameter files, and the input/output files are each noted on a single line as follows. The options shown in parentheses will execute the calculation even if they are not specified.

Windows:

C:\CONFLEX\bin\conflex_dock-1a.exe -par C:\CONFLEX¥par

    (-omp number of parallel threads) -ipro <Protein file name> -ipep <Peptide file name or sequence>

    (-ini <setup file name> -olog <log file name> -opdb <Output PDB file name> -omol2 <Output Mol2 file name> -odir <output folder name>)enter

macOS:

/Applications/CONFLEX/bin/conflex_dock-1a.exe -par /Applications/CONFLEX/par

    (-omp number of parallel threads) -ipro <Protein file name> -ipep  <Peptide file name or sequence>

    (-ini <setup file name> -olog <log file name> -opdb <Output PDB file name> -omol2 <Output Mol2 file name> -odir <output folder name>)enter

Linux:

/usr/local/conflex/bin/conflex_dock-1a.exe -par /usr/local/conflex/par

    (-omp number of parallel threads) -ipro <Protein file name> -ipep  <Peptide file name or sequence>

    (-ini <setup file name> -olog <log file name> -opdb <Output PDB file name> -omol2 <Output Mol2 file name> -odir <output folder name>)enter

The settings for each argument are as follows.

Command line arguments	Description
-par	Specify the directory containing the license and score files. If not specified, the current directory is set.
-omp <numerical value>	Specify the number of threads for parallel computation.
-ipro <File name>	Specify the protein PDB file. If not specified, the calculation is stopped.
-ipep <File name> -ipep <peptide sequence>	Specify the PDB file or array (single or three letter notation) of the peptide. If not specified, the calculation is stopped.
-ini <File name>	Specify the calculation setup file. If not specified, all calculation conditions are executed by default.
-olog <File name>	Set the log file name. If not specified, the file name is set to a combination of the file name specified with -ipro and the file name or array specified with -ipep.
-opdb <File name>	Set the PDB file name to output docking (clustering) results. If not specified, the file name is set to a combination of the file name specified with -ipro and the file name or array specified with -ipep.
-omol2 <File name>	Set the mol2 file name to output docking results (by pose). If not specified, the file name is set by combining the file name specified with -ipro and the file name or array specified with -ipep.
-odir <directory name>	Set the name of the directory to output csv files, etc. If not specified, the directory name is set to a combination of the file name specified with -ipro and the file name or array specified with -ipep.

Examples

As an example, in the macOS environment, let the protein file be protein.pdb and the peptide file be peptide.pdb.

/Applications/CONFLEX/bin/conflex_dock-1a.exe -par /Applications/CONFLEX/par -ipro protein.pdb -ipep peptide.pdb

will output the following files and folders.

protein_peptide/    protein_peptide.log    protein_peptide.mol2    protein_peptide.pdb