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
- 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
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/)
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