MODPROPEP/README at master · narekum/MODPROPEP · GitHub

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  #############################################################################
   __  __  ____  _____  _____  _____   ____  _____  ______ _____
  |  \/  |/ __ \|  __ \|  __ \|  __ \ / __ \|  __ \|  ____|  __ \
  | \  / | |  | | |  | | |__) | |__) | |  | | |__) | |__  | |__) |
  | |\/| | |  | | |  | |  ___/|  _  /| |  | |  ___/|  __| |  ___/
  | |  | | |__| | |__| | |    | | \ \| |__| | |    | |____| |
  |_|  |_|\____/|_____/|_|    |_|  \_\\____/|_|    |______|_|
  A command line version of MODPROPEP with added features

  MODPROPEP: a program for knowledge-based modeling of protein–peptide complexes
  Narendra Kumar and Debasisa Mohanty
  Nucl. Acids Res. (2007) 35 (suppl 2): W549-W555

  Institute of Cancer Sciences
  Epigenetics Unit
  University of Glasgow
  Garscube Estate
  Glasgow G61 1QH

  Report bugs to narekum@gmail.com or narendra.kumar@glasgow.ac.uk

  Copyright 2016 Narendra Kumar

  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; version 3 of the License.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program; if not, see <http://www.gnu.org/licenses/>
  or write to the Free Software Foundation, Inc., 51 Franklin Street,
  Fifth Floor, Boston, MA 02110-1301, USA.


  #############################################################################

  MODPROPEP suite of programs


  1. MODPROPEP score

           __  __  ____  _____  _____  _____   ____  _____  ______ _____
          |  \/  |/ __ \|  __ \|  __ \|  __ \ / __ \|  __ \|  ____|  __ \
          | \  / | |  | | |  | | |__) | |__) | |  | | |__) | |__  | |__) |
          | |\/| | |  | | |  | |  ___/|  _  /| |  | |  ___/|  __| |  ___/
          | |  | | |__| | |__| | |    | | \ \| |__| | |    | |____| |
          |_|  |_|\____/|_____/|_|    |_|  \_\\____/|_|    |______|_|
                                                   ___  ___ ___  _ __ ___
                                                  / __|/ __/ _ \| .__/ _ \
                                                  \__ \ (_| (_) | | |  __/
                                                  |___/\___\___/|_|  \___|

Usage:
MODPROPEP_score.pl < -p PDBFILE -r RECEPTORCHAIN -l LIGANDCHAIN -m SCORINGMATRIX -o outfile > [Options]

Options:
  -h, --help       Print this help

  -p, --pdbfile    Pdb file containing coordinates of protein(receptor)
                   and ligand(peptide) (required)

  -r, --rchain     Receptor chain letter in pdb coordinate file (required)

  -l, --lchain     Ligand chain letter in pdb coordinate file (required)

  -s, --sequence   protein sequence to be scanned in fasta format (required)

  -o, --outfile    name of the outputfile (required)

  -m, --matrixfile Scoring matrix file properly formated (required)

  -d, --distance   Distance for considering two atoms to be in contact in
                   angstroms ( default 4.5)

  -a, --atomtype   Which atom types should be considered for contact between
                   receptor and ligand  (default any)
                   Options:
                   any=any atoms between receptor and ligand
                   cb =c-beta; only C-beta to C-beta distances between receptor
                               and ligand will be considered

  -e, --excludebb  Exclude backbone (sugar-phosphate atoms in DNA; N,C,CA,O
                   atoms in Peptide/proteins) (default F)
                   Options: T (true), F (false)

Examples:
$ perl MODPROPEP_score.pl --pdbfile complex.pdb -rchain A -lchain L \\
       -matrixfile MJ.mat -distance 6 -atomtype CB -o outfile
\or\
$ perl MODPROPEP_score.pl --p complex.pdb -r A -l L -m MJ.mat -d 6 -a CB


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