protein protein docking and MD simulation
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12 months ago

Hii i have two proteins one is small peptide and other is receptor protein, i want to do docking on two proteins and MD simulation. which software and tools are available ?

moleular docking • 246 views
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Please search online for "molecular dynamics simulation software". Using Google effectively is a critical skill for anyone that uses computers.

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Not sure this is a right way to convey a message, especially to a relatively new user. I recall getting slammed as unprofessional for using LMGTFY to make a point.

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LMGTFY is condescending. I do accept that "this is not google" is unnecessary and I have removed that from my comment.

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Just like you are allowing that "this is not google" is unnecessary but not more, I will allow that there are condescending examples of using LMGTFY. Not all of LMGTFY uses are such, and mine for sure wasn't.

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12 months ago
Mensur Dlakic ★ 10k

It is difficult to answer this if you don't know anything about either subject as it appears from your question. Try "molecular docking tutorial" or a similar search in Google - there are nice suggestions at the very top. Briefly, you will need to prepare molecules in proper format, and it helps if you know at least roughly where the docking site is. If you are literally allowing your ligand to dock anywhere, that will take a long time and will not be very accurate. I'd suggest you focus on docking first, as MD simulation of docked complexes is a big can of worms.