Bioinformatics

Secondary Structure Prediction Essay:
It is important to foresee alternate protein structures for knowledge and information regarding protein function. Predicting petty(a) structure is the succeeding(prenominal) step in protein structure prediction if prediction via while analysis does not give secondary structure information.
at that place are threesome main ways in which secondary protein structure can be predicted; these are using statistical methods such as Chou-Fasman, Complex statistical methods such as GOR and third generation methods including PredictProtein, PSIPRED and JPRED.
Statistical Methods
Chou Fasman uses one intercellular substance and looks at the frequency of amino acids in alpha helices, beta-sheets and beta turns. If it is found that a installment 6 amino acids in length has a p(alpha) of 1.03, where P(alpha) is greater than P (Beta), then the successiveness is likely to code for an alpha helix. However if a sequence of well-nigh 5 amino acids in lengths has a p(alpha) of 1.05 where p(beta) is greater than p(alpha), then the sequence is likely to fold as a beta sheet. This method is disadvantageous because it has a q3 of 55% and is naïve, not using any real chemical theorem. Boundaries of secondary structures are therefore not predicted very well.




Complex statistical methods
GOR is an example of a complex statistical method which uses three matrices and refer to residues. These residues carry two pieces of information,; primary sequence and conformation. The line intra-residue is used to describe information about the residue itself, whereas inter-residue refers to the neighbouring residues which match the residue in question. This method therefore takes into account neighbouring amino acids by looking at 8 amino acids in the first place and 8 amino acids after the residue of interest. The Q3 for this method is approximately 73%, although this method does not take into account long-range interactions such as those sometimes seen in beta sheets.
deuce-ace Generation Methods
Third generation methods...If you want to get a full essay, order it on our website: Ordercustompaper.com



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