A standalone suite of programs to estimate the quality of protein-protein interfaces globally as well as locally. SARAMAint plots the distribution of buried amino acid residues at the protein-protein interfaces in the Complementarity Plots (CPint) coupled with the analysis of hydrophobic burial profiles of the same.

SARAMA (Complementarity Plot for globular proteins): https://github.com/nemo8130/SARAMA-updated

CPdock (Complementarity Plot for protein-protein docking): https://github.com/nemo8130/CPdock

http://www.saha.ac.in/biop/www/db/local/sarama/sarama-readme.html

Requires PERL (v.5.8 or higher), and a fortran90 compiler (prefered: ifort) and just one additional package(s) to be pre-installed

1. delphi v.8.3. (http://compbio.clemson.edu/delphi) [executable_name: delphi]

You can either choose to run the single (SARAMA / SARAMAint) or multi-dielctric (SARAMA-multidielctric-delphi / SARAMAint-multidielctric-delphi) version to appropriately set the protein internal dielectric continumm at the interior / or at the interface.

Users are recomended to read additional background literature before implementing the multi-dielctric Delphi-Gaussian mode here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622359/

$ git clone https://github.com/nemo8130/SARAMA-updated
$ cd SARAMA-updated
$ cd SARAMA
$ or
$ cd SARAMA-multidielectric-delphi
$ chmod +x install
$ ./install <fortran90-compiler>  (Default: ifort)

$ git clone https://github.com/nemo8130/SARAMAint-updated
$ cd SARAMAint-updated
$ cd SARAMAint
$ or
$ cd SARAMAint-multidielectric-delphi
$ chmod +x install
$ ./install <fortran90-compiler>  (Default: ifort)

    1. The coordinate (PDB) file for the model

    2. -tar NNN-XXX   (e.g., 100-TYR, 67-PHE etc.)

• The specified target residue must map consistant to the residue sequence number of the input PDB file.
• PDB file MUST contain corrdinates of geometrically fixed Hydrogen atoms
• preferably fixed by REDUCE v.2 or atleast compatible with the REDUCE format (http://kinemage.biochem.duke.edu/downloads/software/reduce/)

Add Hydrogen atoms

You can generate the fasta sequence by using:

$ reduce -trim inp.pdb > input.pdb 
$ reduce -build -DB ~/lib/reduce_het_dict.txt <input.pdb> | awk '$1=="ATOM" || $1=="HETATM"'  >  inputH.pdb

$ ./CompPlot -inp <inputH.PDB> 
$ ./CompPlot -inp <inputH.pdb> -tar <45-THR>
$ ./CPint -inp <inputH.pdb>

where,

• inputH.pdb: The input pdb (coordinate file in Brrokheaven format; http://www.ccp4.ac.uk/html/procheck_man/manappb.html) file

EXAMPLE OUTPUT:

$ cat OUT1psr/1psr.CS

      CS_l: 1.53895, rGb: 0.06081, Pcount:  8.333, Psm:  -0.844, Pem:  -1.288

SARAMA/README.output

SARAMAint/README.output

  Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding
  Sankar Basu, Dhananjay Bhattacharyya, and Rahul Banerjee*
  Biophysical Journal, 2012, 102 (11) : 2605-2614 
  doi:  http://dx.doi.org/10.1016/j.bpj.2012.04.029

The article is avialable online here: http://www.cell.com/biophysj/abstract/S0006-3495%2812%2900503-6