Team:ACIBADEM ISTANBUL/Model

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Giant Jamboree

Model

Protein Production Model



Protein Design Model

1- Protein modelling

Initial protein modelling was done at i-Tasser web server, which is the most used tool for homology-predictive modelling of small molecules. Protein sequence of the desired molecules are just submitted to the web server which gives you probable protein models back. (Just for small peptides under 30 amino acids.) Results are given as .pdb files



2- Protein modifications

Protein modifications are done on Avogadro program. This program allows you to modify your pdb file according to your desire. In the program; methylation, phosphorylation, pegylation, and such modifications can be done easily. Program allows you to use steepest descent algorithm in order to find the lowest energy level of the modified protein. Modified molecules are saved as pdb files again.



3- Docking process

Docking of the small molecules are done with Autodock Vina program. Modified proteins and according macromolecules (venoms) were prepared before docking by Autodocktools program. Same process had been followed for every modified protein. Tutorial from the autodock vina web site was followed for docking.



4- Parameters

Parameters for docking changes for every docking and must be set differently for every molecule. (Molecule coordinates etc.) Only one parameter was set the same for every process which is the spacing for the grid box. 0.010 Angstrom spacing used for every docking. This means for every 0.010 Angstrom on the grid box was tried for the probable ligand-macromolecule interaction.


5- Results

Output of Autodock Vina is pdbqt file which can be read by any molecular viewer such as Pymol, Chimera, or AutoDockTools. For every pdbqt file, there will be a log file. Log files gives the 10 best energy level for interaction of the specific ligand-macromolecule interaction. There will be separate log files for every docking. Potential docking surfaces must be determined beforehand the docking so proper interactions can be chosen.

Docking