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Questions related from Manan Vishvas Desai
We wish to perform a molecular dynamics simulation of cell division protein from a hyperthermophile species at 37 deg cel to check for its stability. Is there a specific analysis in GROMACS for...
11 January 2017 6,323 17 View
During a molecular dynamics simulation i have found salt bridges being format being N(eta) atoms of Arg and OXT atom of Asp. What is the role of OXT atom and is such a salt bridge formation possible?
04 September 2016 4,002 3 View
Is calcium a chaotrope or Kosmotrope? The Hofmeister series shows it to be a kosmotrope, however, some sources refer to it as a chaotrope. Does it behave differently in biological systems as...
18 May 2016 543 6 View
Following a molecular dynamics simulations, one of the results obtained was related to radius of gyration. What is the importance of RoG with regards to protein structure and how to interpret the...
26 August 2015 5,420 13 View
I wish to study binding induced folding in intrinsically disordered proteins during protein interactions using molecular dynamics. I am considering TIP3P water model and Particle Mesh Ewald...
16 July 2015 161 3 View
Do molecular recognition features (MoRFs) observed in disordered region change their conformation on energy reduction? I have been analyzing MoRF segments in a prokaryotic protein, which are...
19 February 2015 2,512 5 View
Is it possible to study or determine horizontal gene transfer or the signs of HGT in evolution using sequence alignment or any other bioinformatics/in silico tools?
30 May 2014 8,089 8 View
While performing protein-protein docking using Haddock, the results included something called restraints violation energy and this value was a positive value. What is this energy and what is its...
22 January 2014 5,794 3 View
Is there any in silico tool/method to study structural dynamics/fluctuations of a highly disordered protein. The protein in question is about 400 residues which has a defined secondary structure...
01 December 2013 7,413 37 View
During Structural superimposition, should one consider RMS values based on C alpha superimposition or backbone superimposition? Which one is preferred and why?
26 November 2013 6,127 4 View
Proteosomes such as GroEL are large complexes that fold-unfold other proteins. Is there any computational tool/method other than Matlab to study folding-unfolding abilities of a particular proteasome?
03 November 2013 5,805 6 View
Is it possible to study protein structure evolution based only on a single domain? For instance, a protein of my interest is a disordered protein with only the C terminal domain being...
07 August 2013 8,753 13 View
Gram negative proteobacteria species has different subgroups namely alpha, beta, gamma delta, epsilon, zeta. Is there any difference in the cell wall composition of proteobacteria subgroups?
25 March 2013 140 0 View
I am comparing the active/catalytic site of two proteins A and B, both belonging to the same family. Both bind to a divalent cation but have entirely different and nearly opposite functions. While...
18 March 2013 8,419 11 View
Is it better to use MUSCLE or CLUSTALW to align amino acid sequences of proteins belonging to the same superfamily?
16 March 2013 1,079 5 View
I am working on a cytoskeletal protein and need to generate free energy landscape models of the protein in its apo form and nucleotide bound form
29 September 2012 3,479 8 View
