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Questions related from Yazan Haddad
I have several protein structure datasets that are each non-redundant and low homology (they average in size between 7k and 14k proteins). My first strategy was to analyze each dataset aside and...
18 June 2020 8,279 0 View
There are over 1200 gene families. Why is it not so simple to align and trace these genes to obtain the consensus first gene? Let's forget the chemistry for a moment and assume that the process...
11 June 2018 1,737 3 View
I have trajectories from Amber in netCDF format (.nc file). I wonder if there is a tool for general rotamer transitions? it will be a lot of labor to make code for each amino acid torsional...
24 March 2017 8,057 1 View
Unless doing a simulation of hemoglobin, I rarely see references to dissolved oxygen or carbon dioxide. Are they so much insignificant in biomolecule interactions?
16 March 2017 8,571 3 View
I was reading that hidden surface with a lot of hydrophobic groups is considered an entropic advantage. To expand the question, is it entropic advantage when buried residues are long chained? Is...
17 February 2017 6,373 3 View
Are pi-pi and cation-pi interactions represented in force fields; such as AMBER, CHARMM, etc..? And if not, how significant can this be in studying protein-protein interactions.. should I be worried?
17 October 2016 2,705 2 View
I want to generate a hypothetical mtz file for my homology structure model (without using cif file). Is there software that can generate mtz file from pdb or xyz coordinates?
16 September 2016 6,961 2 View
It is obvious that when you use a dynamic docking algorithm that such thing would eventually happen. My question is how to justify the results and/or how to avoid this?
23 June 2016 5,898 1 View
