Halide sites

Project availability

You can clone whole repo by standart command:

git clone https://github.com/rostkick/Halide_sites.git

Also if you need to save it without commit-log you schould use:

git clone —depth=1 https://github.com/rostkick/Halide_sites.git

If you want to save only one file (for example without saving example data) you should: 1) copy link of favorite file 2) go to https://minhaskamal.github.io/DownGit/#/home, paste it, and create Download Link.

Dependencies

You should install it manually:

• Anaconda
• FreeSASA

  Preparation

  Create your conda environment from our smk.yml

  conda env create -f smk.yml --name smk

  Activate your environment (some of this should work)

  conda activate smk

  or

  source activate smk

Make sure everything works on --dryrun.

snakemake all -n

How to use

snakemake all

DAG of jobs

Pipeline input

Pipeline automatically creates input consisting of all PDB entries with halide sites

Or you can collect your input by following rule:

Input consist of PDB ID, which separeted by \n:

3VRS
2LH5
6RI4
5EVC
...

You should put the files in the directory data/pdb_ID/, and give them a name according to a strict template pdb_entries_X.txt, where X is (F, Cl, Br, I)

Scripts description

1. rule PDB_par ser(PDB_parser.py) - obtain pdb ID from PDB database
2. rule fetch_structures (fetch_structures.py) - obtain structures from PDB;
3. rule filter (filter.py) - applies filters to PDB structures;
4. rule get_context_data (get_context.py) - applies filters to halide binding sites;
5. rule combine_final_data (parse_context.py) - aggregates data from all halides, then return 2 output files:
   • aggregated information about (model_name, distances, angels, fASA, atom_type, residue_type, water distribution, etc);
   • aggregated information about compositions of amino acids.
6. rule figures_plotting (figs.R) - makes graphic report.

   References

7. Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. https://anaconda.com.
8. Mitternacht, S. FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5, 189 (2016).