CABSdock is a standalone application for molecular docking of peptides to proteins. The CABSdock allows for flexible docking (also with large-scale conformational changes) without knowledge about the binding site. The CABSdock enables peptide docking using only information about the peptide sequence and the protein receptor structure.

References:

• Mateusz Kurcinsk, Michal Jamroz, Maciej Blaszczyk, Andrzej Kolinski and Sebastian Kmiecik
  CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
  Nucleic Acids Research, 2015, Vol. 43, Web Server issue W419–W424 doi: 10.1093/nar/gkv456
• Maciej Blaszczyk, Mateusz Kurcinski, Maksim Kouza, Lukasz Wieteska, Aleksander Debinski, Andrzej Kolinski, Sebastian Kmiecik
  Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking
  Methods Volume 93, 15 January 2016, Pages 72-83 https://doi.org/10.1016/j.ymeth.2015.07.004.
• Maciej Paweł Ciemny, Mateusz Kurcinski, Konrad Jakub Kozak, Andrzej Kolinski & Sebastian Kmiecik
  Highly Flexible Protein-Peptide Docking Using CABS-Dock
  Methods in Molecular Biology, 1561: 69-94, 2017 DOI 10.1007/978-1-4939-6798-8_6.

• CABSdock Github page

• Module Name: CABSdock (see the modules page for more information)
• Unusual environment variables set
  • BC_HOME  installation directory
  • BC_BIN       executable directory
  • BC_SRC       source code directory
  • BC_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ interactive --gres=gpu:v100x:1,lscratch:10 --mem=24g -c16
[user@cn0816 ~]$ module load CABSdock 
[+] Loading singularity  4.1.5  on cn0071
[+] Loading CABSdock 0.9.18  ...

[user@cn0816 ~]$ CABSdock -h
usage: CABSdock [OPTIONS]

CABSdock application is a versatile tool for molecular docking of peptides to proteins. It allows
for flexible docking (also with large-scale conformational changes) and without the knowledge about
the binding site. CABSdock enables peptide docking using only information about the peptide sequence
and the protein protein structure. Additionally many advanced options are available that allow for
manipulation of the simulation setup, the degree of protein flexibility or guiding the peptide
binding etc.

CABSdock method has been first made available as a web server [Nucleic Acids Research, 43(W1):
W419-W424, 2015; web server website: http://biocomp.chem.uw.edu.pl/CABSdock]. The standalone
application [submitted to publication] provides the same modeling methodology equipped with many
additional features and customizable options.

BASIC OPTIONS:
  Basic options needed to run CABS simulation.

  -i INPUT, --input-protein INPUT
    Load input protein structure.

    INPUT can be either:

    [1] PDB code (optionally with chain IDs)
    i.e. '-P 1CE1:HL' loads chains H and L of 1CE1 protein structure downloaded from the PDB database
    [2] PDB file (optionally gzipped)

    Note that only protein chain(s) are extracted from the input file, discarding all non-protein
    molecules.

  -p PEPTIDE, --peptide PEPTIDE
    Load peptide sequence and optionally peptide secondary structure in one-letter code (can be used
    multiple times to add multiple peptides).

    PEPTIDE can be either:

    [1] amino acid sequence in one-letter code (optionally annotated with secondary structure: H -
    helix, E - sheet, C - coil)
    i.e. '-p HKILHRLLQD:CHHHHHHHHC' loads HKILHRLLQD peptide sequence with the secondary structure
    assignment: CHHHHHHHHC

    HINT: If possible, it is always recommended to use secondary structure information/prediction. For
    residues with ambiguous secondary structure prediction assignment it is better to assign coil (C)
    than theregular (H - helix or E - extended) type of structure.

    [2] PDB code (optionally with chain ID)
    i.e. '-p 1CE1:P' loads the sequence of the chain P from 1CE1 protein
    [3] PDB file with peptide's coordinates, loads only a peptide sequence from a PDB file

    '--peptide PEPTIDE' is an alias for '--add-peptide PEPTIDE random random'

  -c FILE, --config FILE
    read options from FILE

PROTEIN OPTIONS:
...
[user@cn0816 ~]$ cp -r $CABSDOCK_SRC/* .  
[user@cn0816 ~]$ python tests/cmap_test.py
.............
----------------------------------------------------------------------
Ran 13 tests in 1.484s

OK

[user@cn0816 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$