Question: What about RMSD ?
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gravatar for chemistry1233
5.5 years ago by
chemistry123340 wrote:

What about RMSD, how important is and where based it, how calculate rmsd. I use autodock vina, I know that rmsd compare my ligands docking with native from rcsb.org. 

but why always first conformation has RMSD 0.00000 and others have  0<RMSD. which must to get as best.

rmsd • 6.3k views
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by chemistry123340
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gravatar for venu
5.5 years ago by
venu6.7k
Germany
venu6.7k wrote:

Question is somewhat obscure (at least to me). 

what about RMSD? You should check this first and I really don't understand what do you mean by 'where based it'. RMSD is a medium to know how much deviation is observed from native conformation after docking has been done . Definitely conformational changes will show up after docking. What do you mean by first conformation and other conformations? Do you mean after docking?  

ADD COMMENTlink written 5.5 years ago by venu6.7k
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gravatar for chemistry1233
5.5 years ago by
chemistry123340 wrote:

I use autodock vina for docking and I get 9 results (conformations) ranked by energy. and always RMSD for first conformation is 0.000 and for others is  RMSD>0.

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1         -7.4      0.000      0.000
   2         -7.4      0.779      1.133
   3         -7.0      1.617      1.993
   4         -6.9     26.631     28.327
   5         -6.6      1.583      1.977
   6         -6.5      3.199      3.974
   7         -6.4      7.415      9.928
   8         -6.3     26.568     27.714
   9         -6.1     27.082     28.571
 

in this example which I should to get as best binding energy from RMSD value.

comparison happen from ligand-protein complex from rcsb.org and my ligands that I use for docking. but what if my ligand is more active than native ligand

ADD COMMENTlink written 5.5 years ago by chemistry123340

calculate RMSD for every conformation and the native one. The one with the lowest RMSD value from the native conformation is the best one, note the binding energy. Compare binding energy of native conformation and your docked conformation. Based on this single (probably simple) result, you can't say your ligand is more active than native ligand. Autodockvina is a good one but but the perfect one. Compare your results with the results from other docking programs. 

ADD REPLYlink written 5.5 years ago by venu6.7k
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gravatar for chemistry1233
5.5 years ago by
chemistry123340 wrote:

Thanks. But why always with vina   first conformation has RMSD 0.0000. as in my example. and my question is should I get as best cornformation, it that has lowest binding enrgy and lowest RMSD value (geenraly RMSD<2 A)

ADD COMMENTlink written 5.5 years ago by chemistry123340

You can select the best conformation among the results of autodock vina but not the best conformation for a particular protein. While searching for poses the program keeps the given conformation as it is and starts selection of poses from there. Thats wh you always get RMSD value 0.

ADD REPLYlink written 5.5 years ago by venu6.7k
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