8 Questions 16 Answers 0 Followers
Questions related from Nor Hasmaliana Abdul Manas
If a his-tagged protein must be eluted from Ni-NTA resin by using buffer with imidazole, how imidazole can just simply be removed from the resin using equilibrium buffer only? Can someone clarify it?
25 August 2016 5,124 3 View
Anyone has any idea how to calculate protein surface charges (electrostatic)? Perhaps any online tools to do that?
01 June 2016 487 4 View
I have run the LIGPLOT, but I keep getting error message: ''LIGPLOT failed. File not found: C:\tmp\lig5519066766696727914\ligplot.drw'' Can anyone help me with this problem? Thank you very much!
11 February 2016 9,562 8 View
In my case, I dock different substrates (ligand) to an enzyme (receptor). Each substrate gives different binding energy. How can I relate the binding energy with the substrate affinity? Is the...
12 July 2015 1,731 10 View
I used AutoDock Vina to dock a substrate (a carbohydrate) into an enzyme active site (a carbohydrase).Is the resulted complex structure (enzyme-substrate) reliable for the analysis of binding...
24 June 2015 5,385 12 View
I did flexible docking using Vina. The output file (pdbqt) consists of the ligand conformation with the flexible residues. How do I combine the output file with my protein in one single pdb file?...
18 November 2014 10,050 10 View
Vina generates one output pdbqt file with many conformations. How can I generate a single pdb file of my protein complex with one of the conformations that I choose from the output pdbqt file?
18 November 2014 1,398 16 View
In Autodock4.2, we can set the number of GA runs for docking. However, in Autodock Vina, there is no option for specifying the number of runs. I was just wondering, how many runs actually Vina do...
18 November 2014 8,854 10 View
