IDD Protein-DNA Filter

A Matlab-based program helps filter FTDock conformers of protein-DNA interaction based on whether the DNA is cut through by the IDD plane.

If you use our software, please cite us:

Chandrasekaran, A., Chan, J., Lim, C., & Yang, L.-W. (2016). Protein dynamics and contact topology reveal protein-DNA binding orientation. Journal of Chemical Theory and Computation, acs.jctc.6b00688. http://doi.org/10.1021/acs.jctc.6b00688

How to use?

1. Extract the IDD.zip file containing the IDD folder

2. Run the following in Matlab:

 addpath('Full path of the IDD folder in the IDD_Filter folder that was extracted in (1)')
 [filtered_conformers_list, IDD_norm, mean_mid_point_transitions, num_transition_points] = IDD_prot_DNA_conformer_filter(FTDock_output_file, prot_pdb_file, dna_pdb_file, num_conformers, filtered_conformers_list_file, output_folder);

Which will generate num_conformers and apply the IDD filter, the filtered conformers list will be written out to filtered_conformers_list_file while the PDB files of the filtered conformers in output_folder.

If you do not want to write out the conformers:

 [filtered_conformers_list, IDD_norm, mean_mid_point_transitions, num_transition_points] = IDD_prot_DNA_conformer_filter(FTDock_output_file, prot_pdb_file, dna_pdb_file, num_conformers, filtered_conformers_list_file);

Optional arguments:

• num_conformers: Set the number of FTDock conformers to filter. Default: '', 4000 FTDock conformers
• filtered_conformers_list_file: Filename to write the list of filtered conformers. Default: '', does not write to file
• output_folder: Folder to write the filtered conformers in PDB format. Default: '', does not write conformers to disk

For more details, in Matlab type:

 help IDD_prot_DNA_conformer_filter

NOTE: The protein MUST be the STATIC molecule and DNA the MOBILE molecule.

See the Example section below for an example on how to do a complete run.

Example

An example is provided in the Example folder. To dock and filter the protein-DNA complexes:

$ cd IDD_Filter/Example
$ Path_to_FTDock_folder/scripts/preprocess-pdb.perl -pdb 1vsr.pdb
$ Path_to_FTDock_folder/progs/ftdock -static 1vsr.parsed -mobile 1cw0_A_DNA.pdb -out 1vsr_1cw0.out

This might take a while. The *.bak files in the folder are the FTDock files generated by us and can be used to compare with the files you have generated.

Open Matlab and change the current working directory to IDD_Filter/Example then:

 addpath('Full path of the IDD folder in the IDD_Filter folder that was extracted earlier')
 [cur_filtered_conformers_list, cur_IDD_norm, cur_mean_mid_point_transitions, cur_num_transition_points] = IDD_prot_DNA_conformer_filter('1vsr_1cw0.out', '1vsr.parsed', '1cw0_A_DNA.pdb', '', '', '');

OR

 [cur_filtered_conformers_list, cur_IDD_norm, cur_mean_mid_point_transitions, cur_num_transition_points] = IDD_prot_DNA_conformer_filter('1vsr_1cw0.out', '1vsr.parsed', '1cw0_A_DNA.pdb');

The above will not write the PDB files of the filtered conformers and the list to file, if you would like to do that, run the following:

 [cur_filtered_conformers_list, cur_IDD_norm, cur_mean_mid_point_transitions, cur_num_transition_points] = IDD_prot_DNA_conformer_filter('1vsr_1cw0.out', '1vsr.parsed', '1cw0_A_DNA.pdb', '', 'File to write list of filtered conformers', 'Path to the folder where the PDB of the filtered conformers will be written to');

You should get back the following output:

	cur_IDD_norm: 0.8847, -0.4642, 0.0430
	cur_mean_mid_point_transitions: -1.7904, 0.9226, 1.5122
	cur_num_transition_points: 4
	The precalculated cur_filtered_conformers_list can be found in cur_filtered_conformers_list.txt

All the output of is stored in 1vsr_1cw0_output.mat.

$ tar -xzf fftw-2.1.5.tar.gz
$ cd fftw-2.1.5
$ ./configure
$ make -j 5 install

$ ./configure --prefix=path_to_other_location
$ make -j 5 install

$ tar -xzf gnu_licensed_3D_Dock.tar.gz
$ unzip IDD.zip
$ cp IDD_Filter/FTDock_patch 3D_Dock/progs/FTDock_patch
$ cd 3D_Dock/progs/
$ patch < FTDock_patch