Installation & Usage

Sections

Requirements

To encode protein structures into matrices, it is necessary to install the DSSP program (http://swift.cmbi.ru.nl/gv/dssp/) to assign secondary structure of proteins and the NumPy package of Python (http://www.scipy.org/install.html) to calculate the vectors and interaxial angles.

Installation - Linux

1. First, download the binary file from "http://swift.cmbi.ru.nl/gv/dssp/".
2. Then, open a terminal and create a symbolic link to DSSP, for example:
   $ ln -s ~/programs/dssp2.0.4/mkdssp /usr/bin/dssp
   or copy it directly to /usr/local/bin or /usr/bin/dssp with cp comand.
3. Next, download the last MOMA version (MOMA_1.1.tar.gz)
4. After, unzip and untar the compressed file (MOMA_1.1.tar.gz):
   $ tar -xzvf MOMA_1.1.tar.gz
5. Finally, open the "MOMA" folder and run "make" command to compile the program that compares matrices.
   $ cd MOMA/
   $ make

Installation - Mac OS X

1. First to compile DSSP on OS X, you should have the latest version of Apple's Xcode and its "Command Line Tools" on your system. Also make sure to have installed "Homebrew" (https://github.com/Homebrew/homebrew/tree/master/share/doc/homebrew#readme). Next, install the boost libraries using "Homebrew":
   $ brew install boost
2. Obtain the DSSP source code from "ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/" We use the 2.0.4 version.
3. Decompress the source code and change to its directory:
   $ tar zxvf dssp-2.0.4.tgz
   $ cd dssp-2.0.4
4. Run "make" command into dssp folder, this should fail with errors:
   $ make
5. Cleanup the cruft leftover from previous make:
   $ make clean
6. Now you have a new file in the current directory "make.config", edit this file with an text editor in lines:
   # Set local options for make here
   BOOST_LIB_SUFFIX = -mt
   BOOST_LIB_DIR = /usr/local/lib
   BOOST_INC_DIR = /usr/local/include/boost
7. Then, edit the file "makefile" and delete the word -static. Save the two files and recompile with:
   $ make
8. Next, create a symbolic link to new mkdssp executable in the current directory, for example:
   $ ln -s ~/programs/dssp-2.0.4/mkdssp /usr/bin/dssp
9. Next, download the last MOMA version (MOMA_1.1.tar.gz)
10. After, unzip and untar the compressed file (MOMA_1.1.tar.gz):
    $ tar -xzvf MOMA1.1.tar.gz
11. Finally, open the "MOMA" folder and run "make" command to compile the program that compares matrices.
    $ cd MOMA/
    $ make

Usage Instructions

1. Create a matrix from a protein structure (in PDB format):
   $ python tableauSSE.py examples/1BL0.pdb
2. Select a protein chain to encode in a matrix of secondary structure elements:
   $ python tableauSSE.py -c A examples/1BL0.pdb
   By default, the output matrix is renamed as "<name of pdb file>-<distance cutoff>.out", for example: "1bl0-20.out".
3. Define distance cutoff in the matrix of secondary structure elements:
   $ python tableauSSE.py -d 25 examples/1BL0.pdb
4. Encode the PDB files within a folder into matrices
   $ python tableauSSE.py -l examples/PDB/
   This command create a matrix for each PDB file within a folder and create a library of matrices outside of folder (renamed as "PDB-20.out" if do not use other parameters).
5. Run "compare" command on a pair of matrices to align with default parameters (g1:-4, g2:-4, C:45)
   $ ./compare examples/1bl0-20.out examples/1aih-20.out
6. Specify combination of gap penalties (g1, g2) and C constant to align the matrices of secondary structure elements
   $ ./compare examples/1bl0-20.out examples/1aih-20.out -5 -5 45
7. Compare a query matrix against a library of matrices
   $ ./compare examples/1bl0-20.out examples/SCOP40-20.out 20
   This command shows a ranking with the 20 top results according to relative similarity (scores sorted in descending order). You can change this value to see more hits.
8. Superpose two PDB files with MOMA
   $ python MOMA.py --cq A --ct A examples/1BL0.pdb examples/1AIH.pdb (run with default parameters)
   $ python MOMA.py --cq A --ct A --g1 -5 --g2 -5 -C 45 -D 25 examples/1BL0.pdb examples/1AIH.pdb
   $ python MOMA.py --cq A --ct A --g1 -4 --g2 -4 -C 90 examples/PDB/2BBM.pdb examples/PDB/1CFC.pdb
   $ python MOMA.py --cq A --ct A --g1 -5 --g2 -5 -C 45 examples/PDB/3L6D.pdb examples/PDB/2UYY.pdb
   $ python MOMA.py --cq A --ct A --g1 -5 --g2 -5 -C 45 examples/PDB/2QX5.pdb examples/PDB/2PM7.pdb
   $ python MOMA.py --cq A --ct A --g1 -10 --g2 -15 -C 45 examples/1CDG.pdb examples/1TIM.pdb
9. See structural alignment with pymol
   $ cd examples/1CDGA_1TIMA/
   $ pymol 1CDGA_1TIMA.py