Can anyone tell me how to model a nano particle using computational softwares (or servres)? I am interested to carry out molecular docking using nanoparticle and protein and for that I need to obtain a particular structure of nanoaprticle. Although the specific structure of the nanoaprticle may not be clearly known, but is there any approximation based model as how to carry out such docking?
Thank you
Dear Mr. Roy,
Molecular docking is a broard area of research. Nano particle docking studies can be carried out with protein. I have experiences to perform the docking study. You may contact with us.
Regards,
Sk. Abdul Amin
Jadavpur University, India.
Thank you. We also carry out protein docking with conventional and modified small molecules to large varieties. But I need some idea about nanoparticle protein docking. Can you kindly let me know or in this forum or send me as message how to approach for this docking?
Ok. Then You may follow the article of Chibber and Ahmad.
Article Molecular docking, a tool to determine interaction of CuO an...
Thanks.
Thank you. But int these papers only the molecule is given as single molecule docking. However suppose ligand within PLGA, chitosan based nanoaprticles are required for dockinng. In that case how can this be modelled?
Nanoparticles are huge in size compared to proteins. Modeling a nanoparticles has so many degrees of freedom that it is very hard to convince anybody the validity of the model. Moreover, there are the capping agents, that covers the surface. One approach you may try is to model a patch of surface (say 10 nm x 10 nm) add some capping agents and then dock the protein on to it followed by molecular dynamics.
For making a metal surface you need to build a unit cell and then extend it into two dimensions, which can be done using softwares like Avogadro.
We have recently published an article where we modeled the interaction of a surface modified gold nanoparticle with DNA using docking and molecular dynamic approaches. You may find that useful.
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