chou fasman method(Mahalakshmi -123011356012)

Chou fasman method

1. SECONDARY STRUCTURE PREDICTION -Chou- Fasman Computational biology-YBT303 SUBMITTED TO PRESENT BY Ms.P.MALA MAHALAKSHMI .B Assistant Professor, Department of Biotechnology 123011356012 Periya maniammai institude of science and technology 2 ND YEAR-MSC vallam,thanjavur Biotechnology Pincode (613403 )

2. CONTENT INTRODUCTION OVERVIEW Prediction Tools and Methods Secondary Structure Prediction Chou- fasman method Conclusion MSQ References

3. INTRODUCTION One of the most common algorithms used for secondary structure prediction constitutes the Chou- Fasman method. This technique divides and in following analyses each amino acid in three different elements , which are a-helices, b-sheets and turns based on already known protein structures. Proteins form one or more determined conformations guided by a number of complicated and reversible non-covalent interactions in order to unfold their their biological functions

4. OVERVIEW Prediction Tools and Methods A great number of structure prediction software tools are developed for dedicated protein features, some among which are disorder prediction, dynamics prediction, structure conservation prediction, etc. Homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction are approaches that help. Each method uses a different level of the protein structure to predict another one. The primary structure is based on the amino acids linear sequence, which when combined in different places and varying numbers, form a different protein.

5. Secondary Structure Prediction The prediction of local secondary structures is facilitated via these tools. These structures are solely based on the amino acid sequence of the protein and their prediction is afterwards compared to DSSP (Define Secondary Structure of Proteins) score , which is calculated based on the crystallographic structure of the protein. It is the standard method used to assign secondary structure annotations to a protein structureThe prediction of local secondary structures is facilitated via these tools.

6. These structures are solely based on the amino acid sequence of the protein and their prediction is afterwards compared to DSSP (Define Secondary Structure of Proteins) score ,which is calculated based on the crystallographic structure of the protein . It is the standard method used to assign secondary structure annotations to a protein structure One of the most well-known and pioneer method is the Chou- Fasman technique. This method provides probabilities of amino acids whether they appear in a-helix, b-sheets or turns.

7. Chou- fasman method The  Chou– Fasman method  is an empirical technique for the  prediction  of secondary structures in   proteins , originally developed in the 1970s by Peter Y. Chou and Gerald D. Fasman .  The method is based on analyses of the relative frequencies of each amino acid  in  alpha helices ,  beta sheets , and  turns based on known  protein Structures solved with X-ray crystallography.

8. From these frequencies a set of probability parameters were derived for the appearance of each amino acid in each secondary structure type, and these parameters are used to predict the probability that a given sequence of amino acids would form a helix, a beta strand, or a turn in a protein. The method is at most about 50–60% accurate in identifying correct secondary structures, which is significantly less accurate than the modern machine learning –based techniques.

9. The turn probability p(t) is determined as : p(t) = pt (j) × pt (j + 1) × pt (j + 2) × pt (j + 3) where  j  is the position of the amino acid in the four-residue window. If p(t) exceeds an arbitrary cutoff value (originally 7.5e–3), the mean of the p(j)'s exceeds 1, and p(t) exceeds the alpha helix and beta sheet probabilities for that window, then a turn is predicted. If the first two conditions are met but the probability of a beta sheet p(b) exceeds p(t), then a sheet is predicted instead. The Chou- Fasman technique is based on statistical data and rules to provide such probabilities

10. CONCLUSION The Chou- Fasman method exports the probabilities for a block of amino acids to be shown in each one of the three elements. Based on the frequencies that are calculated from observation for each amino acid, the probability for the whole sequence is predicted.

11. MCQ 1) What is the primary input for the chou-Fasman method? Amino acid sequence protein 3d structure DNA sequence protein function 2)Which of the following is a parameter used in the chou-fasman method? Hydrophobicity helix- breaking tendency beta-sheet-forming tendency all of the above

12. 3)Who developed the chou-fasman method? pauling and corey anfinsen and ptitsyn chou and fasman 4)What is the output of the chou - fasman method? Tertiary structure secondary structure primary structure quaternary structure 5)What is the significance of the chou-fasman method? predicts protein function identifies protein active sites predicts secondary strucutre from amino acid sequence

13. REFERENCES Chou, P. Y., and Fasman , G. D., 1974a, Conformational parameters for amino acids in helical, ß-sheet and random coil, regions calculated from proteins,  Biochemistry   PubMed Chou , P. Y., and Fasman , G. D., 1974b, Prediction of protein conformation,  Biochemistry   PubMed Chou , P. Y., and Fasman , G. D., 1977, ß-Turns in proteins,  J. Mol. Biol .  PubMed   Chou , P. Y., and Fasman , G. D., 1978, Prediction of the secondary structure of proteins from their amino acid sequence,  Adv. Enzymol .  PubMed Chou , P. Y., and Fasman , G. D., 1979, Prediction of ß-turns,  Biophys , J .  Google Scholar Fasman , G. D., 1985, A critique of the utility of the prediction of protein secondary structure,  J. Biosci .  . Google Scholar

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