Protein Fold
A Deeply Glimpse into Protein Fold Recognition
... proposed protein fold class prediction using neural networks with tailored early-stopping ...the fold class of a protein given solely its primary and it outperformed the standard statistical ...
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PFP RFSM: Protein fold prediction by using random forests and sequence motifs
... of protein tertiary structure is dependent on protein fold ...of protein fold types which takes pri- mary sequence as ...in protein fold prediction. PFP- RFSM and ten ...
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Fast Nonnegative Matrix Factorization and Its Application for Protein Fold Recognition
... Because of its straightforward implementation, NMF has been applied to solve many tasks: information retrieval [4, 5], object classification (faces, handwritten digits, documents) [6–15], sparse coding [16–18], speech ...
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TMFoldWeb: a web server for predicting transmembrane protein fold class
... of fold prediction appears incomplete. The purpose of fold prediction is to transfer the fold (hence function) of the hit protein to the query sequence though the sequence‑fold‑function ...
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Protein Fold Recognition Algorithms-A General Survey
... the protein folding ...the protein threading ...for protein fold recognition have also been used. Typically, protein folding accredits to how a protein amino acid sequences with ...
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Conservation and Divergence of the I-Domain Inserted into the Ubiquitous HK97 Coat Protein Fold in P22-Like Bacteriophages
... The structures of all three I-domains adopt a conserved six-stranded anti-parallel Greek key  -barrel motif (in blue in Fig. 1). The overall structures of the three I-domains are precisely defined, with backbone root ...
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The so far farthest reaches of the double jelly roll capsid protein fold
... by protein, would use a portal with a pack- aging ATPase for genome translocation [13, 33, ...small protein preceding the major coat protein gene. This small protein has no detected similarity ...
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Two-layer SVM classifier for remote protein homology detection and fold recognition
... Remote protein homology detection refers to detection of structural homology in proteins where there are small or no similarity in the ...remote protein homology detection is a classic problem and it aims ...
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Protein Remote Homology Detection and Fold Recognition based on Features Extracted from Frequency Profiles
... established fold benchmark [15] is used for protein fold ...same fold are taken as positive training ...a fold have a very low degree of similarity, this fold benchmark is ...
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Impact of combined acidic and hyperosmotic shock conditions on the proteome of Listeria monocytogenes ATCC 19115 in a time course study
... of protein abundance changes is larger in these cells than the inacti- vated cell population is ...The protein abundance responses are relatively muted (usually less than 3-4-fold) which could be due ...
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A knowledge-based approach to protein structure prediction
... the fold-discriminatory potentials of various sequence- and structure-based features and develop a new SVM-based method for protein fold ...best fold-discrimination and therefore they were ...
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The evolution and functional repertoire of translation proteins following the origin of life
... [20]. Protein and RNA fold modules are highly conserved in evolution ...common fold is thought to be rare ...overall fold architecture is maintained ...of protein fold ...
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BPI-fold (BPIF) containing/plunc protein expression in human fetal major and minor salivary glands.
... in the parotid glands of their fetuses, however, none of the seven parotids evaluated in our study were positive for BPIFA1 or any other marker used, and BPIFA1 has never been detected in adult parotid glands. BPIFA2 is ...
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EBV miR-BART10-3p Promotes Cell Proliferation and Migration by Targeting DKK1
... Figure 7. Effect of DKK1 over-expression in AGS-EBV cells. (A) A real-time RT-PCR analysis of DKK1 mRNA expression was carried out using a SYBR green qPCR kit. (B) DKK1 and β-catenin protein levels were analyzed ...
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Structural Changes in Dengue Virus When Exposed to a Temperature of 37°C
... E protein organization, especially near the 5-fold and 3-fold vertices (molecules A and C, respectively) ...E protein near the 2-fold vertices (B molecule), the two structures showed ...
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Thermodynamic capacity of a protein
... a protein sequence to encode multiple conformations has immediate implications on our under- standing of prions and other multi-stable ...[a protein] adopt? This query not only ad- dresses the issue of the ...
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Suppression of nodulation gene expression in bacteroids of Rhizobium leguminosarum biovar viciae
... levels of NodA, NodI, NodE, and NodO proteins were reduced at least 14-fold in bacteroids compared with cultured cells, whereas NodD protein was reduced only 3-fold.. Northern (RNA) blot[r] ...
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A proteomic analysis of serum-derived exosomes in rheumatoid arthritis
... the protein profiles of serum-derived exosomes among patients with RA and OA and HLs We investigated the protein profiles of exosomes in each of the 43 serum samples by ...204 protein spots were ...
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Biophysical Investigations of the Specificity between Rab GTPases and their Effectors
... Rossmann fold, the tubulin/FtsZ fold, the protein kinase fold, the histidine kinase/HSP90/Topo II fold, the HSP70/RNAse H Fold and the mononucleotide binding fold/P-loop ...
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p53 directly activates cystatin D/CST5 to mediate mesenchymal- epithelial transition: a possible link to tumor suppression by vitamin D3
... expression (Figure 4A). In the presence of CST5 silencing the p53-mediated repression of SNAIL protein was less pronounced than in cells transfected with control siRNAs (Figure 4A). The same effect was observed on ...
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