19 Questions 127 Answers 0 Followers
Questions related from Nikhil Maroli
I would like to assess few enzyme proteins among the organism to understand the difference in their actions. The structure was modelled using homology modeling and same enzyme having different...
05 May 2019 6,466 8 View
Dear Researchers, We synthesised a novel aptamer against a particular protein/peptide target. Its a ssDNA with 87 bp and we would like to submit it to any database such as NCBI. Can anyone tell me...
11 November 2018 407 1 View
Can anyone share simple procedure to evalute the brain delivery or blood brain barrier penetration of a molecule. We dont have much facilities so basic or simple procedures are welcome. We would...
09 September 2018 3,533 0 View
Hi, How i can design an aptamer for a particular protein/peptide in silico, which help to reduce SELEX time and costs.
04 April 2018 3,419 3 View
Dear All, I want to study the role of an amino acid in a protein by mutating it to another amino acid. How will decide or select, the new amino acid? What are the parameters I need to consider?
08 August 2017 3,141 2 View
What is the significance of doing MD of modelled proteins. ?
09 September 2016 2,111 3 View
Is it necessary to add missing residues in proteins before performing docking and MD
09 September 2016 4,245 8 View
Most of the Literature i have seen with NAMD.is there any method or tools in Gromacs to study water and ion permeability of channels in gromacs? from trajectory or otherwise
07 July 2016 10,020 6 View
Hi, For the Molecular dynamics work how and o what pdb of particular protein i should select Example When i search for lysozyme many are coming with the codes 1JUG,1JKB so what are these codes and...
09 September 2015 8,827 2 View
how and what are the files need to be defined? any manual?
06 June 2015 3,089 7 View
In picture given atom and atom type ,what type of naming is it and how i can make this sort of naming from my structure ,what is this A and B etc... I'm from a physics background and I am not...
06 June 2015 4,735 4 View
Residue 1 named LYS of a molecule in the input file was mappedto an entry in the topology database, but the atom CB used inthat entry is not found in the input file. Perhaps your atomand/or...
06 June 2015 4,782 10 View
Hi, I have done energy minimization for my particular structure using gromacs ,after energy minimization what i found is that in my structure one bond is broken, it's a cyclic peptide constitutes...
06 June 2015 9,480 11 View
Hi after installation when i run,mdrun im getting an error Can not open file:topol.tpr can anyone tell me what is this? i installed in two workstations and my laptop, first it was working in my...
06 June 2015 8,571 7 View
Is there any tools to do the same?
06 June 2015 9,950 4 View
What are the best software's for MD and construction of structure please give me a list ,i m looking for buying software's thanks..
05 May 2015 1,131 5 View
How to solve this? please explain
05 May 2015 9,334 3 View
Hi, Anyone can tell me how to add manually residues to topology ,when i use server im getting for optimised structure only. please help me how to get all the parameters required to define...
05 May 2015 8,573 13 View
Dear researchers, Currently we are working on ssDNA aptamers against various diseases in humans. We would like to get supports from the NMR data through collabarations. drop a message if anyone...
01 January 1970 1,049 2 View
