Dileep Vijayan

9 Questions 27 Answers 0 Followers

Questions related from Dileep Vijayan

RMSF for residues?

Hi all, Can any one please suggest me a tool or web server or a script for calculating the root mean square fluctuation for side chain, back bones and all atoms. The protein/DNA structures are...

13 March 2018 7,349 5 View

How to find structurally similar protein?

I have a protein obtained through ab initio modeling. I would like to know whether this protein is exhibiting any kind of structural similarities with other proteins available in the PDB. How I...

02 October 2017 7,228 4 View

Can any one please tell me how to superimpose two quadruplex structures?

I would like to superimpose few quadruplex structures available in the PDB. These structures are either in complexes with proteins or available in free form. The structures are not with similar...

02 October 2017 645 4 View

Can any one tell me where the amyloid beta aggregates are accumulating?

Can any one please tell me where the amyloid beta aggregations (plaques) are depositing? I mean which part of the brain we can find more amyloid plaques? Do anyone have papers on that? I couldn't...

22 May 2017 6,108 3 View

Is it possible to do MM-PBSA calculations from desmond trajectory file?

Hello friends. As a part of one work, I have done molecular docking to explain the in vitro results. I have confirmed the ligand - protein interaction through ITC, Spectrophotometer and enzyme...

12 May 2017 1,383 16 View

FDA approved drugs in SDF format?

Can anyone please tell me from where I can download all FDA approved drugs in SDF format or in smileys format? I have used drug bank and found majority of the approved drugs are not included in...

21 March 2017 6,870 21 View

Can any one suggest me how to compare the active sites of two different proteins?

I am trying to design multi-target directed ligands. I have found some similar common ligands for both proteins. When I docked these ligands I have seen the score is almost similar. But these...

09 March 2017 2,061 2 View

Important water molecules in the protein?

Hello everyone. In my protein the ligand binding site is located on a turn followed by a 3/10 helix (T-3/10) (altogether 10 residues long) which is connecting two anti parallel beta strands. I...

09 March 2017 459 17 View

B factor comparison?

Is it a good idea to compare the b factor of a particular loop of different proteins from same family? I have seen that these proteins are having similar orientation of loops.

19 December 2016 3,148 3 View