I have a protein which has five different components, and these were isolated separately. So is it possible to club these individual fragments together using any tool/software? And if there is/are such software(s), can this structure be used to perform molecular docking against a substrate of my choice?
Yes, it is possible to combine the individual fragments of a protein into a single structure using various software tools. These tools can help you assemble the protein fragments into a complete structure, which can then be used for further analysis, including molecular docking against a ligand.
Here are a few software tools that can help you combine protein fragments:
Modeller: Modeller is a software package widely used for homology modeling and protein structure prediction. It can also be used to combine protein fragments by generating a complete model based on the individual fragments and available structural information. Modeller utilizes comparative modeling techniques to generate the missing regions and optimize the overall structure.
Swiss-PdbViewer (DeepView): Swiss-PdbViewer, also known as DeepView, is a molecular visualization and modeling software. It provides tools for protein structure analysis, manipulation, and modeling. With DeepView, you can manually align and merge the individual fragments to generate a complete structure.
PyMOL: PyMOL is a powerful molecular visualization software that also offers tools for structural modeling and manipulation. It allows you to load the individual fragment structures and manually combine them to create a single protein structure. PyMOL provides a user-friendly interface for visualizing and editing the protein structure. Once you have generated the complete protein structure, you can use it for molecular docking against a ligand of your choice
You should also consider the following before combining protein fragments. Does these fragments function in complex and is implicated in your study? Will the inhibition of the assembled protein elicite an effect that answer the reason for docking/your studies?
Hello dear Nilanjana. It's possible to bring fragments of an individual protein together and do docking. You just have to define one fragment as a ligand and the other as the receptor. Such docking study can be perform through many software such as autodock vina alongside with autodock tools for structure preparation. You can also use chimera which is also a free software like autodock. Autodock is the most popular free software used for docking studies. Schrodinger Maestro and MOE are other examples of popular software for docking and virtual screening, but they are not free. The structure can also be used against the substrate of your choice. The main principle of docking is to bring one molecule (small molecule) termed as ligand in an appropriate cavity (binding site) of another molecule (macromolecule) termed as receptor. This first step is call posing. The second step is scoring which aim to assign a score of affinity (generally in term of binding energy) between the receptor and the ligand.
Thankyou so much for your suggestion! I will definitely check the procedures that you recommended.
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