BND
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2 answers
14 votes
200 views
Finding parameters for a molecule in various forcefields
5 votes

You might want to have a look at acpype which is compatible with GAFF and AMBER-based force fields and probably others.

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2 answers
10 votes
246 views
What are the factors to consider before docking 2 proteins?
5 votes

Another factor to consider might be blind docking or targeted. In this latter, only a region indicated on protein is targeted. In blind docking, the ligand will bind wherever suited on the protein ...

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3 answers
5 votes
86 views
How to extract specific frames/model from a multi model pdb file?
4 votes

file=test.pdb #pdb file frame=10 # frame number to extract x_frame=$(egrep "MODEL.* $frame$" $file) sed -n "/$x_frame/,/ENDMDL/p" $file > ${file::-4}_frame_$frame.pdb output file will be ...

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8 answers
14 votes
2k views
What are some free programs to do docking?
2 votes

Open Drug Discovery Toolkit Open Drug Discovery Toolkit provides nice features of rescoring with different scoring function your docked poses. This is important due to the limitations of scoring ...

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3 answers
10 votes
262 views
How I can analyze and present docking results?
2 votes

A good way to proceed is to use a control in your experiment as with modelling experiment in general. You can, for example, use the co-crystalized ligand or a well-know inhibitor (something ...

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