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Fold recognition
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Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus enhance its conformational flexibility.
15p
viwyoming2711
16-12-2020
16
1
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Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms.
13p
viwyoming2711
16-12-2020
9
1
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A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition
Assigning a protein into one of its folds is a transitional step for discovering three dimensional protein structure, which is a challenging task in bimolecular (biological) science. The present research focuses on: 1) the development of classifiers, and 2) the development of feature extraction techniques based on syntactic and/or physicochemical properties.
11p
viwyoming2711
16-12-2020
16
0
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One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features at fragment level to improve the accuracy of protein fold recognition.
12p
vikentucky2711
24-11-2020
13
2
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Transmembrane proteins (TMPs) are the key components of signal transduction, cell-cell adhesion and energy and material transport into and out from the cells. For the deep understanding of these processes, structure determination of transmembrane proteins is indispensable.
9p
vikentucky2711
24-11-2020
7
1
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GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that GmrS acts as endonuclease and NTPase whereas GmrD binds DNA.
16p
vioklahoma2711
19-11-2020
9
0
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The amino acid sequence of a protein is the blueprint from which its structure and ultimately function can be derived. Therefore, sequence comparison methods remain essential for the determination of similarity between proteins.
15p
vioklahoma2711
19-11-2020
11
0
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Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done before those methods provide reliable fold recognition for proteins whose sequences share little similarity.
14p
viflorida2711
30-10-2020
13
1
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Deep learning is one of the most powerful machine learning methods that has achieved the state-ofthe-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012, it has achieved success in a number of areas such as protein residue-residue contact prediction, secondary structure prediction, and fold recognition.
13p
viflorida2711
30-10-2020
11
2
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Ligand binding by the aryl hydrocarbon receptor (AhR), a member of the bHLH-PAS family of transcriptional reg-ulatory proteins, has been mapped to a region within the second ÔPASÕ domain, a conserved sequence motif ®rst discovered in the Per-ARNT-Sim family of proteins.
6p
research12
29-04-2013
40
2
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Peptidyl-prolylcis–transisomerases (EC 5.2.1.8) catalyse the interconversion of cis and trans peptide bonds and are therefore considered to be important for protein folding. They are also thought to participate in processes such as signalling, cell surface recognition, chaperoning and heat-shock response. Here we report the soluble expression of recombinant Mycobacterium tuberculosispeptidyl-prolyl cis–transisomerasePpiAinEscherichiacoli, togetherwithan investigationof its structure andbiochemical properties....
0p
awards
05-04-2013
33
1
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Upon mutation of Asn130 to aspartate, the catalytic activity of human arginase I was reduced to17% of wild-type activity, theKmvalue for arginine was increased9-fold, and thekcat ⁄Kmvalue was reduced50-fold. The kinetic properties were much less affected by replacement of Asn130 with glutamine.
7p
inspiron33
23-03-2013
43
2
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Micro-myoglobin, the isolated heme-binding subdomain of myoglobin, is a valuable model system for the investigation of heme recognition and bind-ing by proteins, and provides an example of protein folding induced by co-factor binding.
8p
media19
05-03-2013
40
1
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Protein folding in the endoplasmic reticulum is often associated with the formation of native disulfide bonds. Their primary function is to stabilize the folded structure of the protein, although disulfide bond formation can also play a regulatory role.
12p
media19
04-03-2013
25
1
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Bacterial and archaeal endo-b-1,3-glucanases that belong to glycoside hydrolase family 16 share a b-jelly-roll fold, but differ significantly in sequence and in substrate specificity. The crystal structure of the laminarin-ase (EC 3.2.1.39) from the hyperthermophilic archaeonPyrococcus furiosus (pfLamA) has been determined at 2.1 A˚ resolution by molecular replace-ment. ThepfLamA structure reveals a kink of six residues (72–77) at the entrance of the catalytic cleft.
11p
vinaphone15
27-02-2013
33
3
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The twin arginine translocation (Tat) system transports folded proteins across the bacterial plasma membrane. In Gram-negative bacteria, mem-brane-bound TatABC subunits are all essential for activity, whereas Gram-positive bacteria usually contain only TatAC subunits.
12p
vinaphone15
27-02-2013
36
1
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Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành hóa học dành cho các bạn yêu hóa học tham khảo đề tài: Fast Nonnegative Matrix Factorization and Its Application for Protein Fold Recognition
8p
dauphong20
10-03-2012
27
3
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