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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...
01 January 2017 7,624 18 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?
09 September 2016 10,115 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...
05 May 2016 4,349 4 View
Several computational models describe rotational tumbling and rotational relaxation time when describing protein motion and dynamics. What is meant by relaxation time and how is related tumbling?...
10 October 2015 4,206 5 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?
07 July 2015 7,611 3 View
I wish to observe disorder-order transitions using MD. Which would be a more appropriate and accurate forcefield, ff99IDP (AMBER) or OPLS?
07 July 2015 3,473 4 View
Peripatric speciation as type of divergent evolution where a small subpopulation remains within the habitat of an original population but enters a different niche. Is there a way or a method of...
11 November 2014 2,353 1 View
neurons are largely made of a cell body, dendrites and the axon. How did the neuron evolve into such a complex structure? Was the first neuron only a cell body and later developed axon and dendrites?
10 October 2014 7,210 0 View
I am looking to identify single nucleotide polymorphism nucleotide sequences to study how they have evolved/diverged from each other. Is there any bioinformatic tool to identify such changes in 2...
10 October 2014 9,166 1 View
I have noticed that several microtubule-associated proteins contain stretches of glutamine residues. Is there a particular reason for the presence of such Q-rich regions?
10 October 2014 8,891 5 View
Is there as way or approach to understand and study the evolution of intrinsically disordered proteins based on their amino acid sequences using phylogenetics?
10 October 2014 1,698 3 View
Maximum parsimony (MP) has been used extensively for phylogenetic analysis of nucleic acids. However, can it be used for protein sequences? If yes how effective would it be when compared with ML...
10 October 2014 2,502 4 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?
05 May 2014 6,324 9 View
FtsZ is a prokaryotic homolog of eukaryotic tubulin protein. Although being a prokaryotic cell division protein, it is also found in the chloroplast of lower plants such as A. thaliana....
04 April 2014 3,623 3 View
What is the importance of tight turns such as beta turns and gamma turns in protein structure and do they have an impact on protein-protein interactions?
02 February 2014 3,438 4 View
When observing elastic modes of proteins, one of the results files shows deformation energy plot. What is the significance of deformation energy when studying protein dynamics?
01 January 2014 2,049 0 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...
01 January 2014 7,559 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...
12 December 2013 1,503 38 View
During Structural superimposition, should one consider RMS values based on C alpha superimposition or backbone superimposition? Which one is preferred and why?
11 November 2013 8,362 5 View
When compared to NMA, ENM does not require energy minimization of the input protein structure.Thus, is it advisable to perform EM before ENM analysis especially in case of homology modeled...
11 November 2013 1,351 5 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?
11 November 2013 5,223 7 View
Harmonic analysis and approximations made by NMA break down for proteins at physiological conditions. Since this is an important limitation, can NMA be used to study protein dynamics and make...
11 November 2013 2,121 3 View
Proteins domains are considered evolutionary units of protein architecture. Several non-homologous or functionally unrelated proteins tend to share the same domain. Is this convergent or divergent...
09 September 2013 1,495 5 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...
08 August 2013 4,367 14 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?
03 March 2013 1,512 0 View
Is it better to use MUSCLE or CLUSTALW to align amino acid sequences of proteins belonging to the same superfamily?
03 March 2013 3,276 5 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...
03 March 2013 8,980 12 View
Prokaryotic FtsZ (Tubulin homolog) is a GTPase. Its activity and tendency to polymerize is reduced significantly in the presence of excess of calcium.
02 February 2013 800 10 View
Are motions such as hinge motions continuous or episodic in a protein at a given time?
12 December 2012 8,266 0 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?
12 December 2012 3,595 11 View
Several proteins appear to share are some similarity in terms of domains with some other primitive/ancestral proteins. Therefore, is it ok to say that majority of the proteins have been derived or...
11 November 2012 4,982 9 View
I wish to determine a putative hinge region in a protein. Thus, I would like to know what kind of residues form a hinge region and what determines whether a region is suitable to be a hinge in a...
10 October 2012 7,284 16 View
I have aligned protein sequences using Clustal W but how do I confirm/validate whether this alignment is correct? How can one validate a phylogenetic tree?
08 August 2012 2,890 12 View
I am trying to study evolutionary divergence among tubulin family members
04 April 2012 7,104 13 View
