17 Questions 12 Answers 0 Followers
Questions related from Tarun Agarwal
In a protocol book the composition of HPLC eluent is given as - "2mM sodium acetate in 0.75% (v/v) triethylamine:acetonitrile (97:3)". Could anyone suggest me how to prepare it step by step?
16 January 2018 1,546 3 View
Hex shows binding energy of -219.89, while autodock showed for the same -9.89. Can someone clearly state how to defend this difference in the binding energy?? Is it the algorithms they follow that...
14 May 2015 3,413 3 View
I wanted to clone and express few of the nuclear transcription factors (NTFs) in mammalian system. To be more precise, the NTFs are to be secreted in the media from where I have to purify...
24 March 2015 4,270 2 View
I am trying to pull the peptide through the lipid bilayer using GROMACS 4.5.6 double precision but getting the following error while carrying it out. Program mdrun_d, VERSION 4.5.6Source code...
08 December 2014 6,599 5 View
Presently the MDF's are maintained in RPMI media supplemented with 15% FBS, sodium pyruvate and NEAA in a tissue culture flask. But I am finding the cells are undergoing apoptosis after passage 3...
25 November 2014 3,838 3 View
I want to deliver an improperly folded protein (may / may not be improperly folded) into the animal cell. Does it has any chance to get properly folded inside the cell before it get delivered to...
29 October 2014 7,131 13 View
I'm trying CDOCKER module of Discovery studio for carrying out peptide protein docking at a specific site. But it is showing some error. The error includes some problem with the peptide ligand. Is...
14 October 2014 8,743 3 View
I have been trying to carryout simulation of cell penetration of a peptide by pulling it across a lipid bilayer. But as the peptide is moving into the bilayer the bilayer is completely getting...
12 September 2014 5,740 6 View
I have been trying to modify the gelatin by adding the methacrylate group to it using Methacrylic anhydride (94%, Sigma-Aldrich). I followed the given protocol, as shown in many sources of...
11 September 2014 1,935 16 View
I have designed a peptide, carried out its simulation in normal saline using GROMACS and found increase in radius of gyration, along with Trace of the covariance matrix after diagonalizing around...
04 August 2014 7,068 3 View
If no, kindly tell the differences to carry protein simulation.
26 July 2014 9,171 2 View
Suppose if I want to get the RMSD plot of animo acids of an active site of the proteins only, how can I get it using the GROMACS 4.5.6 version? What will the command be, and how should it be...
05 July 2014 4,440 3 View
How and why werethe charges changed in the topology file of the ligand? Also after simulation I found my ligand and protein were far apart from each other (observed in simulation movie; i.e. they...
21 June 2014 9,100 3 View
In addition to hydrogen bond analysis and secondary structure analysis, please also tell me the difference between RMSD and RMSF of backbone and c-alpha. Which has more significance while...
18 June 2014 564 3 View
For a publication purpose what all analyses are crucial while carrying out the molecular dynamic simulation of only protein. What exactly each analysis represent i.e, what is their significance?
17 June 2014 4,083 6 View
I wanted to ask how can we isolate the "protein.pdb" file during MDS run in different time intervals (such as 100ps, 500ps, 1000ps, 5000ps etc...)
10 June 2014 567 5 View
To be more precise in how can we dock the protein onto specific site of DNA? If possible also tell me how could we isolate the structure of DNA sequence (in PDB format).
28 April 2014 3,168 5 View
