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Protein backbone alternation due to insertion/deletion or mutation operation often results in a change of fundamental biophysical properties of proteins. The proposed work intends to encode the protein stability changes associated with single point deletions (SPDs) of amino acids in proteins. The encoding will help in the primary screening of detrimental backbone modifications before opting for expensive in-vitro experimentations. In the absence of any benchmark database documenting SPDs, we curate a dataset containing SPDs that lead to both folded conformations and unfolded state. We differentiate these SPD instances with the help of simple structural and physicochemical features and eventually classify the foldability resulting out of SPDs using a Random Forest classifier and an Elliptic Envelope based outlier detector. Adhering to leave one out cross validation, the accuracy of the Random Forest classifier and the Elliptic Envelope is of 99.4% and 98.1% respectively. The newly defined database and the delineation of SPD instances based on its resulting foldability provide a head start towards finding a solution to the given problem.
This article was published in the following journal.
Name: Journal of proteome research
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A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
The determination of the concentration of a given component in solution (the analyte) by addition of a liquid reagent of known strength (the titrant) until an equivalence point is reached (when the reactants are present in stoichiometric proportions). Often an indicator is added to make the equivalence point visible (e.g., a change in color).
A change to a DNA SEQUENCE that doesn't change the AMINO ACID SEQUENCE of the protein made.
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
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