Question: protein protein docking and MD simulation
0
gravatar for husainbioinfos
6 weeks ago by
pune
husainbioinfos0 wrote:

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 • 92 views
ADD COMMENTlink modified 6 weeks ago by Mensur Dlakic5.4k • written 6 weeks ago by husainbioinfos0
1

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by RamRS27k

Hi, this is not Google.

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.

ADD REPLYlink written 6 weeks ago by Mensur Dlakic5.4k

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

ADD REPLYlink written 6 weeks ago by RamRS27k

I appreciate your prompt response.

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.

ADD REPLYlink written 6 weeks ago by Mensur Dlakic5.4k
0
gravatar for Mensur Dlakic
6 weeks ago by
Mensur Dlakic5.4k
USA
Mensur Dlakic5.4k wrote:

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.

ADD COMMENTlink written 6 weeks ago by Mensur Dlakic5.4k
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