SARAMA

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

Please be redirected to access the following CP versions from the below links:

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

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

A more detailed Documentation is available here:

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/

Installation

$ 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)

The program has just one mandetory input :

    1. The coordinate (PDB) file for the model

The other optional input is a specification of a target residue (executes the program on a single residue alone)

    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/)

Preparatory Step:

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

Run Step:

$ ./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

For a detail and exhaustive list and documentation of output features, see:

SARAMA/README.output

SARAMAint/README.output

Main Reference

  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