Sidra Rafi

10 Questions 32 Answers 0 Followers

Questions related from Sidra Rafi

Can anyone tell me how i can reterive complete bacterial data from KEGG?

I Want to download complete KEGG bacterial data please guide me how i can do that? or if any one have this data kindly send me. its not freely available for academic user too.

02 July 2019 5,675 6 View

How to make large grid box that cover the whole macromolecule in auto-dock4?

Hello, I am using autodock4 for blind docking of ligand-protein.the size of protein is very large, its contain 5 domains. now i want to make large grid box that cover the whole macro-molecule but...

20 May 2016 7,749 8 View

Which tools can plot inter-hydrogen bond interactions graph?

i want to plot total number of inter-molecular H_bond interactions between the drug compounds and target protein like below mentioned...

01 August 2015 957 12 View

Why Gromacs 4.5.6 does not generate .xtc file?

Hello, I am using Gromacs 4.5.6 version for protein ligand MD simulation. i completly follow Bevan La...

07 July 2015 2,553 8 View

How can we calculate RMSD using MOE?

hello, I want to calculate RMSD of docked multi ligand with a protein using MOE. Please can you suggest how I can calculate this?

04 March 2015 3,719 8 View

How do I calculate binding free energy of simulated antigen-antibody structure?

I want to calculate binding free energy of antigen-antibody complex after 30ns MD simulation. I used MMPBSA but it takes approx 12 days for 1 ns (500 frames) of antigen-antibody complex in which i...

19 February 2015 323 14 View

Which is the best computational software to remodel antigen-antibody?

I downloaded PDB ID 4I3S it contains 16 missing residues in heavy chain of antibody as well as in antigen. I want to remodelled it before running the simulation. Which is the best computational...

25 November 2014 6,565 9 View

How can I calculate inter-hydrogen bonding between an antibody and antigen using pymol?

i want to calculate inter-hydrogen bonding between antigen and antibody using pymol. how i can calculate it and how i can get the hydrogen bonding log file?is there any way to get pymol log file...

25 June 2014 5,353 3 View

How can I split a Gromacs .tpr file?

I have 10ns antigen-antibody simulation tpr file . I want to make movie of it by using chimera but its having huge data so my computer get hang. Anybody tell me how I can make movie of it or how I...

06 March 2014 1,526 2 View

How to extract complete name of query as well as complete name of hit from blast result?

I retrieved 100% identical significant alignment query and hits gene id by using SerachIO perl command but I did not get the complete name of that query and hit gi. How can I extract the complete...

24 December 2013 8,808 2 View