Chou, P.Y., Fasman, U.D.: Prediction of protein conformation. Biochem. (1974) 13:211--215  Home/Search   Document Not in Database   Summary   Related Articles   Check

....solid phase [127] Foil was placed over the apparatus to protect iodogen from exposure to light, as it is light sensitive. Evaporation time was approximately 15 minutes. Ovine IFNt or human IFNaA (10 L of 1 mg mL) in 65 L of 0.05 phosphate buffer pH 7. 5 was then placed on the solid phase iodogen [129, 130]. Free Iodine (0.5 Ci) was added to the vial and 34 incubated at room temperature for 5 minutes. Radiolabeling of the interferon molecules was slowed with the addition of excess 0.25 gelatin in 0.05 M phosphate buffer, pH 7.5, which dilutes the reaction mixture. The reaction was stopped when ....

....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 ....

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Chou, P.Y., Fasman, G.D. Prediction of Protein Conformation. Biochem. 1974. 13(2): 222-245.

....Other properties of variation are explored by Rendell Seshu (1994) 3 TEST CONCEPTS Our goal was to produce difficult learning conditions while using realistic concepts. Some concepts were inspired by difficult real world domains. For instance, to predict the secondary structure of proteins, Chou and Fasman (1974) first identify amino acids as formers or breakers of specific secondary structures, and then apply rules such as: start an ff helix after observing four ff helix formers in a sequence of six consecutive amino acids. This M of N rule and similar ones used in this domain involve many patterns over ....

Chou, P. Y., & Fasman, G. D. (1974). Prediction of protein conformation. Biochemistry, 13 (2), 222--245.

....different structure. However, these two concepts are distinguished by concept variation. To create adverse conditions for learning while using realistic concepts, our study used test concepts inspired by difficult real world domains. For instance, to predict the secondary structure of proteins, Chou and Fasman (1974) first identify amino acids as formers or breakers of specific secondary structures, and then apply rules such as: start an ff helix after observing four ff helix formers in a sequence of six consecutive amino acids. This M of N rule and similar ones used in this domain require many combinations ....

Chou, P. Y. and Fasman, G. D. (1974). Prediction of protein conformation. Biochemistry, 13(2):222--245.

.... super secondary structures [Taylor Thornton, 83] domains [Lathrop, 87] The established methods for protein secondary structure prediction include hand crafted expert rules [Lim, 74] biological predictive patterns [Cohen et al. 83, 86] Presnell et al. 92] statistical Chou Fasman theory [Chou Fasman, 74] information theory based GOR method [Garnier et al. 78] More recent methods often make use of inductive learning techniques, whereby a system is trained with a set of sample proteins of known conformation and then uses what it has learned to predict the structure of previously unseen ....

P.Y. Chou& U.D. Fasman. Prediction of protein conformation. Biochemistry 13, 4894-4904.

....four levels, because the assumptions of higher levels may be wrong. If so, we have to proceed the analysis at the lower level. Secondary Structure level Next, we are going up to a higher representational level. First, we change representation of attributes by applying the Chou Fasman method [2] to primary amino acid sequences. Then, we obtain prediction of secondary structure for each amino acid sequence. For example, the 4th to 10th amino acids form ff helix. Based on the above results, we replace the value of each attribute, which is the address of a primary sequence, by the above ....

Chou, P.Y. and Fasman, G.D. Prediction of protein conformation. Biochemistry, 13, 222244, 1974.

....forces primitive representations and makes relations among attributes more relevant. Thus, for instance, molecular biologists form protein folding theories that involve complex relations among amino acids occupying consecutive positions in the protein sequence. In particular, Chou and Fasman [3] use a condition for ff helix formation that requires a sequence of 6 consecutive amino acids containing at least 4 helix formers (which are just amino acids known to favor the formation of helical structures in the process of protein folding) Assuming that 5 of the 20 amino acids used in ....

Peter Y. Chou and Gerald D. Fasman. Prediction of protein conformation. Biochemistry, 13(2):222--245, 1974.

....satisfies an equivalence relation R f . Finally, let jDj denote the cardinality of D, that is, the total number of samples in D. A probabilistic rule of D is defined as a quadruple, R f ff; p d; ff; p , where R f ff; p d satisfies the following conditions: 1) x] R f T D 6= OE; 2) ff = j[x] R f T D)j j[x] R f j ; 3) j[x] R f T D)j jDj ; 4) p : p value of 2 statistics; where p is a p value of 2 statistics when the relation between [x] Rf , D, and U is tested as a contingency table. 2 The intuitive meaning of the above three variables, ff, and ....

....total number of samples in D. A probabilistic rule of D is defined as a quadruple, R f ff; p d; ff; p , where R f ff; p d satisfies the following conditions: 1) x] R f T D 6= OE; 2) ff = j[x] R f T D)j j[x] R f j ; 3) j[x] R f T D)j jDj ; 4) p : p value of 2 statistics; where p is a p value of 2 statistics when the relation between [x] Rf , D, and U is tested as a contingency table. 2 The intuitive meaning of the above three variables, ff, and p value is given as follows. First, ff corresponds to the accuracy measure. For example, if ff of ....

[Article contains additional citation context not shown here]

Chou, P.Y. and Fasman, G.D. "Prediction of protein conformation," Biochemistry, 13, pp.222-244, 1974.

....et al. 1984] and C4.5 [Quinlan, 1993] C4.5, the decision tree system used in this thesis, has been developed over an extended period of time and includes techniques for reducing the effect of noise and generating production rules from trees. 1.5. 3 Secondary structure prediction Chou and Fasman [Chou and Fasman, 1974] and Lim [Lim, 1974] proposed the secondary structure prediction problem almost twenty years ago. Recently, researchers have used artificial intelligence techniques to attack the problem [Qian and Sejnowski, 1988, Holley and Karplus, 1989] Zhang et al. Zhang et al. 1992] describe a system that ....

Chou, P. and Fasman, G. (1974). Prediction of protein conformation. Biochemistry, 13:222--244.

....have shown that such interactions play a significant role in the formation of actual protein structure. Information concerning these long range interactions constitutes the state information necessary to adequately address this prediction problem. We have encoded the rules from the Chou Fasman [4] protein secondary structure prediction algorithm into an expert network and augmented this expert network with knowledge about longer range amino acid interactions. Results of protein secondary structure prediction experiments show that the addition of state knowledge to existing algorithms ....

....structure elements into a tertiary structure [6] Thus, many have viewed the prediction of the secondary structure of a protein as a necessary step toward prediction of its tertiary structure. Many algorithms have been developed for protein secondary structure prediction. The Chou Fasman algorithm [4] is a widely used algorithm for protein secondary structure prediction. Its prediction accuracy, however, is estimated to be between 50 [3] and 58 [16] 4.1 The Chou Fasman Algorithm In the Chou Fasman approach to protein secondary structure prediction, two conformational parameters, a helix ....

P. Y. Chou and G. D. Fasman. Prediction of protein conformation. Biochemistry, 13(2):222--245, 1974.

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Chou, P.Y., Fasman, U.D.: Prediction of protein conformation. Biochem. (1974) 13:211--215

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Chou, P.Y., Fasman, G.D. Prediction of protein conformation. Biochemistry 13:222--245, 1974.

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Chou, P.Y., Fasman, G.D. Prediction of protein conformation. Biochemistry 13:222--245, 1974.

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