2019
DOI: 10.1016/j.csbj.2018.12.005
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Residue Adjacency Matrix Based Feature Engineering for Predicting Cysteine Reactivity in Proteins

Abstract: Free radicals that form from reactive species of nitrogen and oxygen can react dangerously with cellular components and are involved with the pathogenesis of diabetes, cancer, Parkinson's, and heart disease. Cysteine amino acids, due to their reactive nature, are prone to oxidation by these free radicals. Determining which cysteines oxidize within proteins is crucial to our understanding of these chronic diseases. Wet lab techniques, like differential alkylation, to determine which cysteines oxidize are often … Show more

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Cited by 12 publications
(9 citation statements)
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“…Probe molecules with a center of mass inside this FVE will not overlap with the atoms of the polymer. The FreeSASA program [39], which is widely used in the analysis of internal cavities in biological systems [41][42][43], was used to analyze the surface of pores.…”
Section: Procedures For Analysis Of Fvementioning
confidence: 99%
“…Probe molecules with a center of mass inside this FVE will not overlap with the atoms of the polymer. The FreeSASA program [39], which is widely used in the analysis of internal cavities in biological systems [41][42][43], was used to analyze the surface of pores.…”
Section: Procedures For Analysis Of Fvementioning
confidence: 99%
“…Therefore, the secondary structure alone is not sufficient to account for the susceptibility of Cys residues to oxidize. Indeed, many structural parameters influence the Cys-OH susceptibility, such as sequential distance to the nearby cysteine, solvent accessibility, p K a, or secondary structures. Finally, three to six peptides containing a derivatized Cys-OH were detected for the other proteins, indicating that these Cys sites are more sensitive to endogenous oxidation. Therefore, this method could be used to provide a valuable insight into the relationship of protein structure and susceptibility to oxidation.…”
Section: Results and Discussionmentioning
confidence: 99%
“…RAM is constructed from n-nearest amino acid distances sequentially from the lysine residues. RAMseq (Residue Adjacency Matrix from sequence data) is an alias of RAM and can simply be calculated from raw protein sequence without the need for any other information like 3-D coordinates or the secondary structure [ 46 ]. The matrix is of 20 by n dimension, which is a result of taking the distance of the target lysine residue to the first, second, third, fourth, and n-th closest amino acid residue of each type in the sequence.…”
Section: Methodsmentioning
confidence: 99%
“…The matrix is of 20 by n dimension, which is a result of taking the distance of the target lysine residue to the first, second, third, fourth, and n-th closest amino acid residue of each type in the sequence. The value of n in this work is taken as six, since it is anticipated to work well on different types of datasets [ 46 ]. The distance in RAM is obtained by taking the index of the amino acid and subtracting it with the index of the lysine residue, up to the n-th amino acid index of the same type.…”
Section: Methodsmentioning
confidence: 99%