SS3D

Sequence Similarity 3D

SS3D is a bioinformatics tool for combining sequence and structure alignment data, evaluating the Sequence Similarity in 3D space between two proteins. Such comparisons are useful for a plethora of purposes such as determination of conserved positions, and explaining different functionalities of proteins that evolved from a common ancestor.

For more information about this tool, check the paper here.

Installation

OS X & Linux:

The only dependences are the sdt14 library itself, and the gcc compiler. You can install it using the following command:

sudo apt install build-essential

You can also use other compilers, just change the 'CC' variable present at the top of the makefile. After downloading/cloning the repository, just enter the folder and type the command:

make

It will create an executable called 'ss3d' inside the folder.

Windows:

It should be easier to import the repository as a new project and compile it using Code::Blocks, Visual Studio or any c++14 IDE/Compiler.

Usage

To get a quick overview of the required and optional parameters, type:

./ss3d help
or
./ss3d -h

SYNOPSIS

ss3d [-a [.pdb]] [-b [.pdb]] [-o [.xvg/.pdb]] [-dist ] [-skip ] [-rad ] [-min ] [-mat ] [-dup] [-norm] [-bfac] [-raw]

OPTIONS:

Obligatory options to specify input & output files:

-a

      Structural file in .pdb format of the first protein.

-b

      Structural file in .pdb format of the second protein.

-o

      Output text file in .xvg or .pdb format.

Other options:

-dist

      The maximum distance to be considered a contact between two alpha carbons, in Ångströms.
      (default distance is 10 Ångströms)

-rad

      The maximum search radius for identifying alpha carbons around a contact, in Ångströms.
      (default radius is 10 Ångströms)

-skip

      Exclude this number of residues within the search radius upstream and downstream in primary
      sequence of the alpha carbon involved in the contact. Used to diminish the contribution of
      sequentially proximal residues in the scoring. (default skip is 3, which will exclude
      6 residues total: the three previous and three subsequent to the one involved in the contact).

-min

      Minimum (absolute) number of common residues between the two proteins around a particular contact
      for it to be accepted. (default is 1 residue[s]).

-mat

      Select the substitution matrix to be used to evaluate the score. The default matrix is blosum62.
      The options are:
      pam250 - The PAM250 matrix.
      blosum62 - The BLOSUM62 matrix.

-dup

      Duplicates the matrix in a mirrored fashion.

-norm

      Normalizes the result to be between 0 and 1.

-bfac

      Maps the score value to the B-factor of the first protein PDB.

-raw

      Produces a raw text file containing the local alignment for each contact, ignoring the
      parameters ``-bfac``, ``-dup`` and ``-norm``, if present.

For examples and a step-by-step tutorial, please refer to the Wiki.

Quick test the SS3D

To quickly test the SS3D tool, we will assume that you have gnuplot and vmd previously installed on your computer.

Access the "tutorial" folder and type the following into the terminal:

Generate matrix

../ss3d -a 1a5r_processed_renumbered.pdb -b 1ubq_processed_renumbered.pdb -o text-output -norm -dup
gnuplot gen_matrix.gnu

Visualize pdb with SS3D coloring:

../ss3d -a 1a5r_processed_renumbered.pdb -b 1ubq_processed_renumbered.pdb -o pdb-output -norm -bfac
vmd -e view_bfactor.vmd

Meta

Igor Daniel M. Lima – igor.sj13@gmail.com

Distributed under the GNU GPL-3.0 license. See LICENSE for more information.

https://github.com/IgorLima/

Contributing

1. Fork it (https://github.com/0x462e41/SS3D/fork)
2. Create your feature branch (git checkout -b feature/fooBar)
3. Commit your changes (git commit -am 'Add some fooBar')
4. Push to the branch (git push origin feature/fooBar)
5. Create a new Pull Request