Prevelige, P., Fasman, G.D. Chou-Fasman Prediction of Secondary Structure: in Prediction of Protein Structure and the Principles of Protein Conformation, ed. G.B. Fasman. Plenum, New York. 1989. 1-91.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....were formulated by comparing Chou Fasman (CF) secondary prediction results to those obtained using the GarnierOsguthorpe Robson (GOR) secondary structure prediction method. Chou Fasman and GOR predictions were calculated using the PeptideStructure computer program (Genetics Computer Group, Inc. [129 131]. Lower case letters denote regions where the structure prediction models did not coincide or predictions were weak. Peptide Name Peptide Sequence Secondary Structure IFNAR2(1 38) ISYDSPDYTDES CTFKISLRNFRSI LSWELKNHSIVP T TURN BETA helix BETA IFNAR2(34 67) SIVPTHYTLLYTI MSKPEDLKVVK NCANTTRSFC ....

....and secondary structure predictions of the synthetic intracellular domain peptides of IFNAR2. Secondary structure predictions were formulated by comparing Chou Fasman (CF) secondary prediction results to those obtained using the GarnierOsguthorpe Robson (GOR) secondary structure prediction method [129 131]. Chou Fasman and GOR predictions were calculated using the PeptideStructure computer program (Genetics Computer Group, Inc. Lower case letters denote regions where the structure prediction models did not coincide or predictions were weak. Peptide Name Peptide Sequence Secondary Structure ....

Prevelige, P., Fasman, G.D. Chou-Fasman Prediction of Secondary Structure: in Prediction of Protein Structure and the Principles of Protein Conformation, ed. G.B. Fasman. Plenum, New York. 1989. 1-91.

....at the end of Section 3. Another direction is exploring ways to incorporate additional partial information that scientists have about the structure of proteins. For example, scientists appear able to predict the secondary structure of portions of proteins with high but not perfect accurary [11, 5], and it would seem useful to be able to utilize these predictions in the global optimization algorithm in some manner. ....

P. Prevelige Jr. and G. D. Fasman, Chou-Fasman Prediction of the Secondary Structure of Proteins, in Prediction of Protein Structure and the Principles of Protein Conformation, G. D. Fasman, ed., Plenum Press, New York, 1989, pp. 391--416.

....networks have been used to predict the secondary structure of a protein. Both algorithms are concerned only with the classification of the secondary structure of each amino acid in the protein, and will be discussed briefly below. 3.2. 1 The Chou Fasman Algorithm The Chou Fasman algorithm [PF89] is a statistical algorithm. Using X ray crystallograhic technology, Chou and Fasman examined structures of a number of proteins in their native states, and tabulated the number of occurrences of a given amino acid in an ff helix, a fi sheet, and random coil. From this, the conformational ....

....in that type of structure. These conformational parameters are essentially measures of a given amino acid s preference to be found in ff helix, fi sheet, or random coil. Based on these parameters, Chou and Fasman formulated a set of empirical rules for predicting protein structure (page 394, PF89] Using these rules, one is able to predict the secondary structure of a protein with an accuracy of about 50 percent. The limited accuracy of the predictions is believed to be due to the relatively small number of proteins from which the conformational parameters are calculated. Also, ....

Peter Prevelige, Jr. and Gerald D. Fasman. Chou-Fasman Prediction of the Secondary Structure of Proteins. In Gerald D. Fasman, editor, Prediction of Protein Structure and the Principles of Protein Conformation, chapter 9, pages 391--416. Plenum Press, New York, 1989.

....be divided into ones that use biological knowledge (and are non learning methods) and those that use a learning mechanism. Non Learning Methods The three most widely used approaches in the biological literature [Fasman89] for predicting protein secondary structure are the Chou Fasman [Chou78, Prevelige89] Robson [Garnier89, Robson76] and Lim [Lim74] algorithms. Chou Fasman relies on information 26 concerning the likelihood for each type of amino acid to be part of a particular secondary structure. This information is summed over local areas of the protein to determine the likelihood for that ....

....that we implemented and tested on the Qian and Sejnowski test data exhibit 58 accuracy (see Table 4) The Lim method [Lim74] is the only one that tries to account for long range interactions; it uses a stereochemical theory of globular proteins secondary structure. Later solutions [Garnier89, Prevelige89] include theories of a fourth type of secondary structure, b turns, which usually are classified as coils. The main advantage of FSKBANN over these algorithms is that while FSKBANN contains some of the biological information, it also has a mechanism for learning. Learning Methods A number of ....

P. J. Prevelige and G. Fasman, "Chou-Fasman prediction of the secondary structure of proteins: The ChouFasman -Prevelige algorithm," in Prediction of Protein Structure and the Principles of Protein Conformation, G. Fasman (ed.), Plenum Press, New York, 1989, pp. 391-416.

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2. Prevelige, J., P & G. D. Fasman (1990). Chou-Fasman prediction of the secondary structure of proteins. Prediction of Protein Structure and the Principles of Protein Conformation. G. R. Fasman. New York, Plenum Press: 391-416.

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