Re: [DIYbio] protein consensus sequence recognition site prediction software

Hey Bruno,

     Unless there is an already determined interaction motif it is not very feasible to predict binding sites from amino acid sequences alone. Even with the protein structures the problem is extremely complicated because it is a three dimensional search. Most programs out there even if they do suggest they might be able to help have usually only been verified on extremely small and particular training sets.

     If you don't have a structure you are in bad starting spot. There are things like covariation analysis(looking for regions of the protein that vary or don't vary together) and trying to use that to predict spots that could be important in binding but still not great. If you haven't already you should create a homology model of the protein using something like SWISS Model(http://swissmodel.expasy.org/). Once you have that you can look for possible binding regions through analysis. Proteins tend to interact using loops or helices through salt bridges or hydrophobic surfaces. Use some or all of these servers to narrow things some maybe(http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/). After that the only real way to test is trial and error using site directed mutagenesis and mutating the protein and measuring binding between the protein and its ligand(binding partner).

     Molecular dynamics won't really help in this situation because the search space is so massive. You can't just throw two proteins(or even a protein and small molecule) into an MD simulation and hope they bind, they won't. Most MD simulations are for understanding thermodynamics and not kinetics(binding is a kinetic event though it involves thermodynamics) because without doing fancy techniques and extrapolating alot the timescale of MD simulation is in nanoseconds to low microsecond(even with the best super computers).

     If the binding effects an actual pathway that creates a phenotypic change you are doing great. Then you can just knock out the endogenous gene in yeast and and put it in a plasmid then using that system screen a bunch of mutants. If there is no great phenotypic change things become much more complicated. You would need to do binding assays, which most likely involves pull downs unless you have access to purified protein.

Hope this helps,
     Josiah Zayner
     http://the-odin.com





On Tuesday, June 14, 2016 at 10:00:22 AM UTC-7, Hiro Protagonist wrote:

Thanks for the answers,

I already used PFAM earlier on to identify the catabolic domain, which actually was pretty helpful.
I used SPARKSX FOLD Recognition (http://sparks-lab.org/yueyang/server/SPARKS-X/) to gain Pdb models, however I am not quite aware of how trustworthy these predictions are.
I'm going to check out PISA and VMD later on, thanks again for the input ^^

I'm aware of http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html but I think you need a pdb in the database or to provide your own. If you don't have an experimentally proved protien folding have you looked at in silico fold prediction?

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