In your current opinion, can we use molecular docking method to make an early prediction of CRISPR effectiveness to attach to the target gene?
Example: I'd like to predict, which gRNA (that proposed by E-CRISPR software) or which Cas endonuclease type that can effectively attach on the target gene?
Yes, you can predict it with our current knowledge in computational biology. Molecular docking is not a proficient tool for reaching your goal but you can use a more sophisticated technique in molecular modeling approaches which is called molecular dynamics.
As its name implies, this method assess the dynamic behavior of each biomolecule you want to evaluate over a period of time. The way in which the proteins interact with each other, the amount of energy required to dissociate the protein-protein complex and also the amount of time in which the two proteins remain in contact with each other can be estimated by a high amount of precision by this in silico method.
So you can run a molecular dynamics simulation on every condition you want and then compare your results in terms of energy, stability and many other thermodynamical parameters.
You might want to look at some related piece of researches done recently in this area;
Preprint Molecular simulations have boosted knowledge of CRISPR/Cas9: A Review
Article Dynamics changes of CRISPR-Cas9 system induced by high fidel...
Article Deciphering Off-Target Effects in CRISPR-Cas9 through Accele...
@ Ivan Tjahja Pranata, I don't think the proposed method will work as this will require complete genomic context (means nucleosome organisation, other protein and RNA binding) of sgRNA recognition site.
The molecular docking primarily provides information about interaction of two molecules by considering hydrophobic, Vander Wall and other forces as well as stearinc hinderance imposed by the 3D structure of the participating molecules. While CRISPER technique changes the hene or physiology of the organism, both are entirely different aspects!
Interesting question. CRISPER/Cas9 system consists of two components the Cas9 protein that cuts DNA and guide RNA to recognize the sequence to be edited, so the target sequence is already known, with no room for much prediction.
sgRNA is designed based on primary/nucleotide sequence of target sequence but if the target sequence is accessible for binding of sgRNA or not depends on conformation of DNA and its binding to various proteins like histones...Any software that can predict DNA conformation in the target sequence surely can help to predict the efficiency of sgRNA binding to target, but I am not sure there is such software currently!
Yes, you can predict it with our current knowledge in computational biology. Molecular docking is not a proficient tool for reaching your goal but you can use a more sophisticated technique in molecular modeling approaches which is called molecular dynamics.
As its name implies, this method assess the dynamic behavior of each biomolecule you want to evaluate over a period of time. The way in which the proteins interact with each other, the amount of energy required to dissociate the protein-protein complex and also the amount of time in which the two proteins remain in contact with each other can be estimated by a high amount of precision by this in silico method.
So you can run a molecular dynamics simulation on every condition you want and then compare your results in terms of energy, stability and many other thermodynamical parameters.
You might want to look at some related piece of researches done recently in this area;
Preprint Molecular simulations have boosted knowledge of CRISPR/Cas9: A Review
Article Dynamics changes of CRISPR-Cas9 system induced by high fidel...
Article Deciphering Off-Target Effects in CRISPR-Cas9 through Accele...
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