Team:Technion Israel/Software
Software tool
We worked hard for many months to successfully redesign the ligand binding site of the E. coli Tar chemoreceptor. This feat was done using the Rosetta software suite by following the protocol presented in "Rosetta and the Design of Ligand Binding Sites" (1). The work we have achieved can be expanded into other receptors and ligands, and can be of use for other researchers.
Our software tool offers fellow scientists the ability to create their own custom chemoreceptors by redesigning the Tar ligand binding site,
and without needing to tackle the many challenges of Rosetta. One can do so in two ways:
1) Using a local installation of Rosetta (preferably on a computer cluster).
2) Online, with the form below.
See the Computational Design page for more explanations about the use of the software, and see the wet lab results of our designs at the results tab.
Fig. 1: The geometry of the commercial fluidic chip
Using a local installation
We supply a zip file for a Linux system with all necessary scripts to successfully run the redesigning automatically. This script is used only as a framework for working with Rosetta, to successfully run it you are required to download and install the following software: Rosetta, BCL, OpenBabel, Python and a protein visualization program such as UCSF Chimera or PyMol.
Installation: Download our software to Linux operation
system and unzip it on the computer running the above programs, in the same folder you wish to save your design work. Edit the path to the programs you just installed in 'runRosetta.sh' file, under the 'define variables' section, and you are ready to go.
Run the main program running the software is 'runRosetta.sh'. Run command for initial help:
./runRosetta.sh -h
The program is divided into steps, according to the steps presented in the protocol "Rosetta and the Design of Ligand Binding Sites" (1):
1. Pre-relax the protein. Run command:
./runRosetta.sh -s 1 -r <receptor file name WITHOUT extension>
2. Prepare the ligand. Run command:
./runRosetta.sh -s 2 -l <ligand file name WITHOUT extension>
3.Place the ligand into the protein. This is the only step which cannot be done automatically. Follow the instructions at the attached pdf
file: "Step3.3-Place_the_ligand_into_the_protein.pdf"
4. Run Rosetta design. Run command:
./runRosetta.sh -s 4 -l <ligand file name WITHOUT extension> -r <receptor file name WITHOUT extension> -m <number of output models>
5. Filter designs. Run command:
./runRosetta.sh -s 5
The software offers default filtration, but this is not suitable for any ligand or receptor. The filters can be easily changed in one of the
files '<results/interfaces>_metrics.config'. To remove a filter just delete it from the config file. To add a filter just add it in the
same format as the others in the config file (the column number is the one in the respectively csv score file).
6. Run new cycle. Run command:
./runRosetta.sh -s 6 -l <ligand file name WITHOUT extension> -r <receptor file name WITHOUT extension> -m <number of output models>
For more information see 'README.txt' file in the source zip file.
Using online form
If you do not have access to a Linux machine, or simply do not wish to deal with Rosetta, we offer an easy way you can still get your redesigned chemoreceptor. All you need to do is to fill out this form, and we will do the rest. We'll send you the result through the mail in the next few days.
Note that this is possible only for redesigning the Tar ligand binding domain to bind your desired ligand. If you wish to redesign a different receptor contact us through the mail: technionigem2016@gmail.com.
References:
1. Moretti, R., Bender, B.J., Allison, B. and Meiler, J., 2016. Rosetta and the Design of Ligand Binding Sites. Computational Design of Ligand Binding Proteins, pp.47-62.
