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