rising accuracy of protein secondary structure prediction

... Determination of protein secondary structure using factor analysis of infrared spectra Biochemistry 29, 9185–9193 21 Byler, D.M & Susi, H (1986) Examination of the secondary structure of proteins ... natural deconvolution of circular dichroism curves of proteins Protein Eng 4, 669–679 ´ Dousseau, F & Pezolet, M (1990) Determination of the secondary structure content of proteins in aqueous solutions ... Estimation of the protein secondary structure Biopolymers 30, 1273–1280 11 Manavalan, P & Johnson, W.C (1987) Variable selection method improves the prediction of protein secondary structure from...

Ngày tải lên: 16/03/2014, 18:20

... reliable protein secondary structure prediction, ” Protein Science, vol 5, pp 2298–2310, 1996 [8] O B Ptitsyn and A V Finkelstein, “Theory of protein secondary structure and algorithm of its prediction, ” ... and J M Thornton, Prediction of supersecondary structure in proteins,” Nature, vol 301, pp 540– 542, 1983 [10] A A Salamov and V Solovyev, Prediction of protein secondary structure by combining ... [54] for the three secondary structure labels, as well as the overall Q3 and SOV score (let us recall that SOV measures the accuracy of the prediction in terms of secondary structure segments...

Ngày tải lên: 22/06/2014, 23:20

... animals of generation 1001 on average had 20 offspring, whereas parents of previous generations on average had two offspring The generation 1002 produced one more generation of 1000 offspring ... identification of all pairs of base haplotypes with an IBD probability among them of > limitIBD; 2) clustering of all pairs of haplotypes identified in step 1, summing the mutual off-diagonal elements ... already decreased the number of haplotypes to 10% of the initial number Accuracy and bias of predicted total breeding values Accuracies of total predicted breeding values of animals with phenotypes...

Ngày tải lên: 14/08/2014, 13:21

... 175:1264-1266 Ball LA: Secondary structure and coding potential of the coat protein gene of bacteriophage MS2 Nat New Biol 1973, 242:44-45 Hasegawa M, Yasunaga T, Miyata T: Secondary structure of MS2 phage ... the results are not obviously biased by the inclusion of long sequence Protein function and secondary structure prediction The attributes of mouse gene products were obtained from the Gene Ontology ... Liu C: Statistical correlation between protein secondary structure and messenger RNA stem-loop structure Biopolymers 2004, 73:16-26 Creighton TE: Proteins: Structure and Molecular Properties 2nd...

Ngày tải lên: 14/08/2014, 14:22

... number of correct predictions/number of total predictions C, correlation coefficient P(x), number of correct predictions in class x/number total predictions in class Q(x), number of correct predictions ... probability of correct predictions [P(x) in Table 1] P(x) gives the accuracy of the prediction of the x class with respect to the overall amount of total predictions made for that class The prediction ... classification of proteins database for the investigation of sequences and structures J Mol Biol 247, 536–540 Kabsch, W & Sander, C (1983) Dictionary of protein secondary structure: pattern of hydrogen-bonded...

Ngày tải lên: 21/02/2014, 15:20

... Therefore, the error of the secondary structure change is much lower than the error of the absolute secondary structure determination The decomposition of truncated Ras in solution and of membrane-bound ... 5913 Secondary structure of Ras bound to lipid bilayer J Guldenhaupt et al ¨ Table X-Ray and NMR-based secondary structure of Ras in comparison with the protein spectra curve-fitting results of ... is easier to compare the corresponding number of amino acids, instead of the percentages of secondary structure Overall, the secondary structures of truncated and lipidated Ras are in very good...

Ngày tải lên: 07/03/2014, 04:20

... atoms: Ct of the C-terminus, Cc of Asp and Cd of Glu, and Og of Tyr Positive unit charges were added at the following atoms: Nt of the N-terminus, Nf of Lys, Cf of Arg, and Nd or Ne of His (depending ... 24 NMR structures of our final ensemble of dimer structures of RIIa D/D Dielectric smoothing at the protein solvent interface [20,21] was used, with an ion exclusion layer around the ˚ protein ... with cutoff total energy value at 240 kcalÆmol)1, comprising the 24 best RIIa D/D structures was used for further analysis (Fig 1) A superposition of the backbone of the final ensemble of 24 structures...

Ngày tải lên: 08/03/2014, 22:20

... activation loop of JAK2, so that in the absence of JAK2 the KIR would consist of an extended loop structure or be completely unstructured and separate from the globular core of the protein, so it ... part, by the rate of turnover of the SOCS proteins Expression of the SOCS proteins is induced directly by STAT binding to the appropriate promoters Rapid destruction of the SOCS protein is also ... performed at 298 K Solutions of 10– 25 lm SOCS3 in the cell were titrated by injection of a total of 290 lL of 80–200 lm of the gp130 peptide The heat of dilution of the gp130 peptide into buffer...

Ngày tải lên: 16/03/2014, 14:20

... reduction of the protein activity (Fig 1B) accompanied by degradation of the protein (data not shown) Structure and dynamics of an antifungal protein Exposition of 104 conidiaÆmL)1 to lgÆmL)1 of PAF ... The anatomy and taxonomy of protein structure Adv Protein Chem 34, 167–218 36 Wilmot CM & Thornton JM (1988) Analysis and prediction of the different types of beta-turn in proteins J Mol Biol 203, ... mediates the binding of the protein to structures of the outer layers of the target organism or exerts its function intracellularly [6,12] In conclusion, the solution structure of PAF has been disclosed...

Ngày tải lên: 29/03/2014, 23:20

... to a variety of secondary structure states, each of which is relatively stable under its given conditions It is demonstrated that the extreme variability of the secondary structure of the peptide ... may be compared to that of a partlyfolded molten globule structure of a protein like a-lactalbumin [23] In that case, the collapse of a core region of partly-folded protein structure gave rise to ... changes in the secondary structure of Ab(140) observed at concentrations in the range of 04 mm SDS or LiDS The amide IÂ region in the IR spectrum is indicative for the secondary structure of the peptide...

Ngày tải lên: 30/03/2014, 02:20

... Fraction of consensus of prediction [F(preds)] as a function of the number of contributing predictions [N(c-preds)] (B) Fraction of consensus of prediction [F(c-preds)] as a function of the redundancy ... will provide us with more and more structures of proteins with very low sequence identity with proteins of known structure The task of predicting the function of a protein is exceptionally interesting ... predictions; GOC, number of GO cellular component predictions; BIND, number of binding predictions; PT, number of post-transcriptional modification predictions; NA, not applicable The number of...

Ngày tải lên: 30/03/2014, 10:20

... use of a flexible structure comparison method that overcomes many of the problems of comparing protein structures that may exhibit only weak similarity 1.1 Structural Hierarchy The aspect of protein ... 406–425 15 Henikoff, S and Henikoff, J G (1992) Amino acid substitution matrices from protein blocks Proc Natl Acad Sci USA 89, 10,915–10,919 Protein Structure Comparison 19 Protein Structure Comparison ... sequences CABIOS 8, 275–282 Dayhoff, M O., Schwartz, R M., and Orcutt, B C (1978) A model of evolutionary change in proteins, in Atlas of Protein Sequence and Structure, vol 5, suppl 3, National...

Ngày tải lên: 08/04/2014, 12:52

... methods for prediction of secondary structure and topology of membrane proteins, as well as prediction of their tertiary structure A list of useful resources for membrane protein structure prediction ... techniques Chapter (Local Structure Prediction of Proteins) covers protein secondary structure prediction, supersecondary structure prediction, prediction of disordered SVNY330-Xu-Vol-I x November ... problem of protein structure comparison and applications, and computational approaches for aligning two protein structures Applications of the structure structure alignment algorithms to protein structure...

Ngày tải lên: 27/06/2014, 10:20

... set of all human proteins in HPRD consisted of 8582 proteins and was used to see the accuracy of purely random predictions, while the second set of 830 proteins was used to observe the effect of ... deposition of massive numbers of protein structures into the Protein Data Bank, with over 60,000 protein structures currently deposited [11] In combination with documented protein- protein interactions, ... human proteins as "HIV-similar" proteins No proteins of unknown structure were considered Interaction Prediction We found known interactions between HIV-similar proteins and target human proteins,...

Ngày tải lên: 12/08/2014, 04:20

... Sparsification of the Rivas and Eddy Algorithm The class of structures predicted by the R&E algorithm [8], here called class of R&E structures, is the most general RNA secondary structure prediction ... programming algorithms for RNA secondary structure prediction with pseu-doknots Discrete Appl Math 2000, 104:45-62 11 Deogun JS, Donis R, Komina O, Ma F: RNA secondary structure prediction with simple ... number of base pairs in a R&E structure of S, because the recursions perform the same decompositions as the original R&E recursions Note that W(i, j; k, l) is the maximal number of base pairs in structures...

Ngày tải lên: 12/08/2014, 17:20

... ecificity Figure Results of protein- protein interaction prediction by PIC Results of protein- protein interaction prediction by PIC (a) Receiver operating characteristic (ROC) curves of PIC for S cerevisiae ... o-localizing protein pairs Figure pairs that co-localize Enrichment of PIC predictions by interacting protein pairs versus protein Enrichment of PIC predictions by interacting protein pairs versus protein ... for S cerevisiae is made of protein pairs that not colocalize Therefore, it may be possible that PIC recognizes subcellular localization of proteins instead of protein- protein interactions To...

Ngày tải lên: 14/08/2014, 08:21

... the sum of DGV and RPG remained constant, regardless of the level of residual polygenic variance Figure shows the influence of the sires’ EBV on the DGV of validation bulls The R2 values of the ... shows the observed variance of estimated DGV defined as the sum of SNP marker effects and the variance of DGVt, which was defined as the sum of DGV and the estimate of the residual polygenic effect, ... GEBV, we can conclude that the impact of the assumed percentage of residual polygenic variance on accuracy is limited Regression of conventional deregressed EBV of the validation bulls on their GEBV...

Ngày tải lên: 14/08/2014, 13:21

... Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins Protein Eng 1996, 9:27-36 Eisenhaber B, Bork P, Eisenhaber F: Sequence properties of ... buried surfaces in proteins J Mol Biol 1976, 105:1-12 Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJ: Prediction of protein secondary structure and active sites using the alignment of homologous ... Torkkila E, Riikonen P: Accuracy of protein flexibility predictions Proteins 1994, 19:141-149 Krigbaum WR, Komoriya A: Local interactions as a structure determinant for protein molecules: II Biochim...

Ngày tải lên: 14/08/2014, 14:21

... adaptability of 3DBLAST for the initial scan of large protein structure databases; conversely, detailed structure alignment tools often align two structures slowly but accurately Because of basic ... SCOP-108 the distributions search searchlisting 976 proteins23 of X-ray structures on proteins forof the representative 3D structure codes 38 proteins structures overview representative segments structedkind ... Bystroff C, Baker D: Prediction of local structure in proteins using a library of sequence -structure motifs J Mol Biol 1998, 281:565-577 Kolodny R, Koehl P, Guibas L, Levitt M: Small libraries of...

Ngày tải lên: 14/08/2014, 18:20

Ngày tải lên: 13/11/2014, 10:21