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Questions related from Dr Thirumal Kumar D
Hello Researchers The support for g_mmpbsa is not extended for the latest versions of gromacs (2020). I have already performed 200ns simulations and wish to perform PBSA calculations. What could...
29 September 2020 10,340 2 View
I want to study the interaction analysis of chromium 6 with the proteins. There is a single molecule of chromium 6+ in PubChem and ChEMBL. I want it as a 3D lattice structure. How to get it?
16 August 2020 4,505 0 View
I have made a protein-protein docking and performed simulations using Gromacs. I want to make a hydrogen bond study on it using gmx hbond. 1. The docked complexes residues are not in a continuous...
29 June 2020 2,304 3 View
I have made a protein-protein docking and performed simulations using Gromacs. I was to make MMPBSA study on it. 1. The docked complexes residues are not in a continuous sequence. (eg. Chain A has...
29 June 2020 2,799 6 View
Is it valid to compare the wild type protein against the protein that has been truncated due to stop codon mutation using molecular dynamics simulations?
04 May 2020 1,894 3 View
Consider, I have a set of drugs and proteins. I am curious to know if there are any Cytoscape plugin that can map a network between these set of protein and drugs.
29 April 2020 9,225 2 View
It would be very helpful if someone can send me a link or text containing the list RNA dependent RNA POLYMERASE (RdRp) inhibitors.
21 March 2020 5,900 4 View
I wish to study the change in interaction of the small molecule with the protein in respective to change in pH. GROMACS focuses most on protonation state and not directly on pH. So how can I...
26 February 2019 8,028 4 View
We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...
03 April 2018 8,014 0 View
Can someone suggest free online/offline tool to predict the drugliness of the multiple small compounds in sdf format? I tried DrugLito, but it is predicting incorrect values. So I am looking for...
16 June 2017 4,169 0 View
When there is a set of parameters for drug-likeness such as MW, LogP, HBD, HBA, etc., why are some commercially available drugs which are known to best don't satisfy it?
09 June 2017 559 4 View
I have a compound and as a first line analysis, I need to find whether this compound possess anticancer activity or not. How to predict it through in silico approach? Are there any web servers or...
11 May 2017 4,291 4 View
I usually add counter ions (Na or Cl) to neutralize system during dynamics but if a protein is already in neutral condition with a condition "No ions to add and no potential to calculate", what is...
17 March 2017 9,042 3 View
I have a native and mutant PDB files. How to find the percentage of alpha helix, beta sheet, turns etc., from the pdb file (not with the FASTA sequence)
17 November 2016 4,789 3 View
We have found few proteins in the cell (not human) and a drug to treat the cell. Is there an insilico way to find on which protein does my drug interacts (eg. Cytoscape)?
25 September 2016 1,054 14 View
What difference makes exactly between turns and loops? Is there a visualization software to differentiate between loops and turns (Not the helix and sheets).
29 August 2016 5,980 9 View
I am studying a protein which has Cysteine in position 261 and there are reports on PTM at this position and converting to oxoalanine. There are other reports mention cys261arg mutation to be...
01 January 1970 2,502 2 View
In an attempt to make an interaction study, which could have a more in-depth understanding of protein bearing mutations? RAS protein with a mutation bound to GTP or RAS protein with a mutation...
01 January 1970 3,541 1 View
There is Traditional Chinese Medicine Database which contains the compounds from each plants used in treating disease. Similarly, are there any database for Indian medicines?
01 January 1970 8,862 3 View
