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Theory:
• Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the secondary structures of proteins and nucleic acid sequences based only on knowledge of their primary structure.
• For proteins, this means predicting the formation of protein structures such as alpha helices and beta strands, while for nucleic acids it means predicting the formation of nucleic acid structures like helixes and stem-loop structures through base pairing and base stacking interactions.
• Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence that is the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse problem of protein design.
• Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry, it is highly important in medicine and biotechnology.
• The GOR method, named for the three scientists who developed it- Garnier, Osguthorpe, and Robson-is an information theory-based method developed not long after Chou-Fasman. It uses more powerful probabilistic techniques of Bayesian inference.
• The GOR method takes into account not only the probability of each amino acid having a particular secondary structure, but also the conditional probability of the amino acid assuming each structure given the contributions of its neighbors (it does not assume that the neighbors have that same structure).
• The original GOR method was roughly 65% accurate and is dramatically more successful in predicting alpha helices than beta sheets, which it frequently mispredicted as loops or disorganized regions. Later GOR methods considered also pairs of amino acids, significantly improving performance.
Procedure:
• Respective protein sequences of human cox2 (NP_000954.1) in Fasta format was retrieved from NCBI (ncbi.nlm.nih.gov).
• Log in to http://npsa-pbil.ibcp.fr/cgi-bin/npsa_au..._gor4.html
• Paste the respective sequences in the given input boxes.
• Click run.
• Results were displayed as soon as the given job completed.