12 Questions 9 Answers 0 Followers
Questions related from Ayzeha Kalsoom
I have 2 sequences, I have modeled them by using I-tassar, as homology was so less as 20%, so can't use modeller suite. I have got 5 sequences from I-Tassar, ab-initio modelling, after...
10 October 2013 2,882 7 View
I found a paper regarding the work we wanted to do. The receptor they have used is same as we have decided to target but the ligands are not same, we have our own novel compounds belonging to the...
10 October 2013 306 8 View
After drawing structure of chemical compound I wanted to show or label the carbon oxygen hydrogen atom, like C1. C2 O5 H3 means a position of a particular atom. How can I do this in marvin sketch...
09 September 2013 7,116 1 View
Simulations after docking
09 September 2013 9,549 11 View
I wanted to know, what changes will occur, if a replace or remove of a functional group of ligand at give specific site and put it on other position with that ligand, my ligand have steroids and...
09 September 2013 3,283 3 View
my protein consist of 4 chains, A B C and D, my binding pocket is on 2 chains A AND C , can i delete the B an D for carrying out the docking studies, as my binding pocket lies on A and C chain?
07 July 2013 657 9 View
I have a set of 30 chemically similar compounds, i want to do virtual screening, should i start docking studies after drawing their structure or should perform other any other analysis...
07 July 2013 1,025 7 View
The MD simulations using gromacs 96 force field was done on a compound obtained after semi-flexible docking and flexible docking. The protein was also simulated in water. Comparing the docking...
06 June 2013 9,692 5 View
How can I draw a hydrophobic interaction between ligand and receptor protein using VMD?
06 June 2013 9,292 3 View
I have simulated the protein in water and 2) protein with ligand now I want to check the g energy in gromacs for both system individually and then combine to one plot. How could I do this?
05 May 2013 4,680 7 View
I have simulated the protein-ligand system by using the Gromacs force-field 43a1 after obtaining the docking results for semi-flexible and flexible docking. My ligand is a steroid, and they...
05 May 2013 1,325 5 View
I am just new to gromacs. Can anyone please help me in correcting these charges for the itp file, i.e. how to adjust them? These have been generated by prodrg, I have read the article for...
04 April 2013 8,675 1 View
