ProTSPoM: Prediction of change in Gibbs free energy from Single Point Amino Acid mutations (SPMs) in protein structures

For any doubts and suggestions contact-
Computations in Structural, Molecular, and Systems Biology Lab
Department of Computer Science and Engineering
Indian Institute of Technology, Kharagpur
West Bengal, India
Email: anupambanerjee@iitkgp.ac.in / pralay@cse.iitkgp.ac.in


PLEASE DOWNLOAD AND UNZIP ProTSPoM.tar.gz in the current directory.

This folder contains the codes and the input files necessary to predict the change in Gibbs free energy from SPMs in proteins.

Software requirement:
	a.	TMalign- You can get the TMalign executable from- https://zhanglab.ccmb.med.umich.edu/TM-align/
	b.	Stride- You can get the Stride executable from- http://webclu.bio.wzw.tum.de/stride/		
	d.	HBPlus- You can get the HBPlus executable from- http://www.ebi.ac.uk/thornton-srv/software/HBPLUS/
	e.	Scwrl- You can get the Scwrl executable from- http://dunbrack.fccc.edu/scwrl4/SCWRL4.php
	f.	FoldX- You can get the FoldX executable from- http://foldxsuite.crg.eu/academic-license-info

Download and install them in your system if they are not already available. Make sure that the programs are running standalone and can be integrated with the given code.

Provide the absolute path of the softwares and relevant folders in runinfo.txt file. An example file is provided as runinfo_example.txt. 
Please note that runinfo_example.txt is prepared in our system. Your system specific location should be in runinfo.txt.
DO NO ALTER THE SEQEUNCE AND THE FORMAT OF the runinfo.txt file.

Unzip the provided pdb folder and provide the path of the pdb folder in the PDBdb field of the runinfo.txt file.

In order to run ProTSPom without considering homology information (Runtime in seconds and performs slightly worse than while considering evolutionary information)-

Run- perl ProTSPom.pl Absolute_path_to_runinfo.txt Absolute_path_to_ProTSPom's_bin Absolute_path_to_folder_containing_input chain_id residue_number native_AA mutated_AA 0

Place the PDB file whose change in Gibbs free energy you want to compute in a folder and rename it as input.ent. An example file can be found in the workdir_example folder.
Ensure the following in the input PDB file-
a. Place only the ATOM records corresponding to a single chain ID.
b. There should be no chain break (backbone discontinuity) in the PDB files. You can fix it using ITASSER or MODELLER softwares.
c. The residues shouldn't have multiple occupancies.
d. The atom and residue index should be contiguous.
e. There should be a chain ID in the relevant location in the PDB files.

The '0' provided as the last argument correspond to ProTSPoM not considering homology information.

Example- perl ProTSPom.pl /home/user/ProTSPom/runinfo.txt /home/user/ProTSPom/bin /home/user/ProTSPom/workdir A 112 I K 0


In order to run ProTSPom considering homology information (Runtime in minutes)-

Run- perl ProTSPom.pl Absolute_path_to_runinfo.txt Absolute_path_to_ProTSPom's_bin Absolute_path_to_folder_containing_input chain_id residue_number native_AA mutated_AA 1

Place the PDB file whose change in Gibbs free energy you want to compute in a folder and rename it as input.ent. Follow the same constarints as mentioned above.
Additionally, provide a file named input_blast.txt in the same folder. In order to prepare input_blast.txt do-
i.  Run blastp (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) on the sequence of the input protein with the default parameters (Expect threshold=10 and Word size=6)
ii. Once the run has completed, download the alignemnt file in text format (Look under Download->Alignmnet->Text). Rename the file as input_blast.txt.

The '1' provided as the last argument correspond to ProTSPoM considering homology information.

Example- perl ProTSPom.pl /home/user/ProTSPom/runinfo.txt /home/user/ProTSPom/bin /home/user/ProTSPom/workdir A 112 I K 1

The output file named output.txt containing the predicted change in Gibbs free ernergy (or with relevant error messages) will be generated in the same folder in which the 
input file (input.ent) is present. 

Ensure that your python (version Python 2.7.15 used) has the Scikit-learn (version 0.20.2. used), numpy (version 1.15.4 used) and pickle (version 2.0 used) packages installed in it.