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Questions related from Manan Vishvas Desai
In a book chapter authored by Kim Sneppen from the book titled " Physics in Molecular biology; Kim Sneppen and Giovanni Zocchi; Cambridge University Press (2005)", it has been mentioned that...
18 June 2025 8,443 3 View
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 6,407 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 4,078 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 610 6 View
An accurate determination of diffusion coefficient for a protein would be to consider a 3-dimensional diffusion coefficients namely, translational and rotational diffusion coefficients. My...
17 October 2015 1,045 4 View
i wish to calculate Zimm-Bragg helix-coil parameters following a MD simulation. To do that i need to determine the waiting time. how to do that?
08 October 2015 7,624 4 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 5,488 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 211 3 View
I wish to observe helix-coil transformation using MD simulation. What would be the minimum time scale for the simulation to observe such conformational transitions?
14 July 2015 9,258 4 View
Beta turns are common found motifs in proteins. In general, they assume a coil-like conformation. Preliminary analysis using Profunc revealed that the extreme c-terminal region (of a protein we...
12 July 2015 9,543 2 View
I wish to study helix to coil transformation in a protein when its unbound and when it interacts with other proteins. For molecular dynamics what would be an effect parameter choice for such...
04 July 2015 6,458 1 View
Proteobacteria is broadly divided in different groups–alpha,beta, gamma, delta, epsilon, and zeta. Evolution shows that beta and gamma are paralogous and considered unique as compared to other...
12 April 2015 9,536 6 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 2,562 5 View
While there is extensive literature that provides an answer to the above question, both types have been known to be associated with neuronal MTs (microtubules); however, only for type II or...
02 October 2014 8,691 1 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 8,155 8 View
Extreme regions of proteins usually appear to be disordered and when modeled they appear as random coils or when checked with Profunc tool they appear to be tight turns (mostly beta turns). In...
28 March 2014 4,488 11 View
To determine the effect of mutation on a putative hinge region, I had mutated the single reside and determined the stability energy. The predicted value of stability appeared to be 2.83 Kcal/mol....
29 January 2014 1,738 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 5,865 3 View
Can alpha helix act as a hinge region in a protein structure or only random coils/loops can act or form the hinge region?
12 January 2014 1,873 13 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 7,469 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 6,177 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 5,855 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 8,827 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 198 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 8,485 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 1,145 5 View
Phosphorylation site in a particular protein using bioinformatic tools
09 January 2013 8,681 5 View
It is always necessary to use 1000 bootstraps during tree building or can lesser values be used. If so , then how can one determine the bootstrap values during tree building?
19 December 2012 2,244 11 View
Are motions such as hinge motions continuous or episodic in a protein at a given time?
15 December 2012 7,266 0 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 3,546 8 View
