A Computational Approach To Classify HIV Secondary Structure Of Enzymes

10.5580/5b1 ◽  
2011 ◽  
Vol 5 (2) ◽  
Keyword(s):  
Secondary Structure ◽  
Computational Approach

scholarly journals A Computational Approach for the Identification of Small GTPases Based on Preprocessed Amino Acid Sequences

2009 ◽  
Vol 8 (5) ◽  
pp. 333-341 ◽  
Author(s):  
Dominik Heider ◽  
Jessica Appelmann ◽  
Tuygun Bayro ◽  
Winfried Dreckmann ◽  
Andreas Held ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Secondary Structure ◽  
Prediction Accuracy ◽  
Biological Activities ◽  
Small Gtpases ◽  
Computational Approach ◽  
Small Gtpase ◽  
Amino Acid Sequences ◽  
Network Cluster

The prediction of essential biological features based on a given protein sequence is a challenging task in computational biology. To limit the amount of in vitro verification, the prediction of essential biological activities gives the opportunity to detect so far unknown sequences with similar properties. Besides the application within the identification of proteins being involved in tumorigenesis, other functional classes of proteins can be predicted. The prediction accuracy depends on the selected machine learning approach and even more on the composition of the descriptor set used. A computational approach based on feedforward neural networks was applied for the prediction of small GTPases. Consequently, this was realized by taking secondary structure and hydrophobicity information as a preprocessing architecture and thus, as descriptors for the neural networks. We developed a neural network cluster, which consists of a filter network and four subfamily networks. The filter network was trained to identify small GTPases and the subfamily networks were trained to assign a small GTPase to one of the subfamilies. The accuracy of the prediction, whether a given sequence represents a small GTPase is very high (98.25%). The classifications of the subfamily networks yield comparable accuracy. The high prediction accuracy of the neural network cluster developed, gives the opportunity to suggest the use of hydrophobicity and secondary structure prediction in combination with a neural network cluster, as a promising method for the prediction of essential biological activities.

scholarly journals Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop ‘G4 Kissing’ interaction

2020 ◽  
Vol 48 (11) ◽  
pp. 5907-5925 ◽  
Author(s):  
Jonathan D Williams ◽  
Dominika Houserova ◽  
Bradley R Johnson ◽  
Brad Dyniewski ◽  
Alexandra Berroyer ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Chromosomal Rearrangements ◽  
Higher Order ◽  
Computational Approach ◽  
Stem Loop ◽  
Genome Wide ◽  
Switch Regions ◽  
Regulatory Capacity ◽  
Genomic Regions

Abstract Mammalian antibody switch regions (∼1500 bp) are composed of a series of closely neighboring G4-capable sequences. Whereas numerous structural and genome-wide analyses of roles for minimal G4s in transcriptional regulation have been reported, Long G4-capable regions (LG4s)—like those at antibody switch regions—remain virtually unexplored. Using a novel computational approach we have identified 301 LG4s in the human genome and find LG4s prone to mutation and significantly associated with chromosomal rearrangements in malignancy. Strikingly, 217 LG4s overlap annotated enhancers, and we find the promoters regulated by these enhancers markedly enriched in G4-capable sequences suggesting G4s facilitate promoter-enhancer interactions. Finally, and much to our surprise, we also find single-stranded loops of minimal G4s within individual LG4 loci are frequently highly complementary to one another with 178 LG4 loci averaging >35 internal loop:loop complements of >8 bp. As such, we hypothesized (then experimentally confirmed) that G4 loops within individual LG4 loci directly basepair with one another (similar to characterized stem–loop kissing interactions) forming a hitherto undescribed, higher-order, G4-based secondary structure we term a ‘G4 Kiss or G4K’. In conclusion, LG4s adopt novel, higher-order, composite G4 structures directly contributing to the inherent instability, regulatory capacity, and maintenance of these conspicuous genomic regions.

Application of Modified Bloch Waves to Image Analysis of Extended Linear Defects

1974 ◽  
Vol 32 ◽  
pp. 402-403
Author(s):  
S. Nakahara ◽  
D. M. Maher
Keyword(s):  
Image Analysis ◽  
Computational Approach ◽  
Dislocation Loops ◽  
Plane Wave Expansion ◽  
Dynamical Equations ◽  
Bloch Waves ◽  
Linear Defects ◽  
Imperfect Crystal ◽  
Localized Defects ◽  
Defective Crystals

Since Head first demonstrated the advantages of computer displayed theoretical intensities from defective crystals, computer display techniques have become important in image analysis. However the computational methods employed resort largely to numerical integration of the dynamical equations of electron diffraction. As a consequence, the interpretation of the results in terms of the defect displacement field and diffracting variables is difficult to follow in detail. In contrast to this type of computational approach which is based on a plane-wave expansion of the excited waves within the crystal (i.e. Darwin representation ), Wilkens assumed scattering of modified Bloch waves by an imperfect crystal. For localized defects, the wave amplitudes can be described analytically and this formulation has been used successfully to predict the black-white symmetry of images arising from small dislocation loops.

Characterization of Tamm-Horsfall Urinary Glycoprotein

1973 ◽  
Vol 31 ◽  
pp. 420-421
Author(s):  
John P. Robinson ◽  
J. David Puett
Keyword(s):  
Electron Microscopy ◽  
Circular Dichroism ◽  
Secondary Structure ◽  
Quaternary Structure ◽  
Normal Adult ◽  
Morphological Properties ◽  
Adult Males ◽  
Circular Dichroïsm ◽  
Urinary Glycoprotein

Much work has been reported on the chemical, physical and morphological properties of urinary Tamm-Horsfall glycoprotein (THG). Although it was once reported that cystic fibrotic (CF) individuals had a defective THG, more recent data indicate that THG and CF-THG are similar if not identical.No studies on the conformational aspects have been reported on this glycoprotein using circular dichroism (CD). We examined the secondary structure of THG and derivatives under various conditions and have correlated these results with quaternary structure using electron microscopy.THG was prepared from normal adult males and CF-THG from a 16-year old CF female by the method of Tamm and Horsfall. CF female by the method of Tamm and Horsfall.

Steroid metabolomics: a rapid computational approach for accurate differentiation of inborn disorders of steroidogenesis

2019 ◽  
Author(s):  
Elizabeth S Baranowski ◽  
Sreejita Ghosh ◽  
Cedric HL Shackleton ◽  
Angela E Taylor ◽  
Beverly A Hughes ◽  
...  
Keyword(s):  
Computational Approach

Identification of the genetic signature of vascular calcification in patients with type 2 diabetes mellitus by a computational approach

2020 ◽  
Author(s):  
Francisco Andújar-Vera ◽  
Cristina García-Fontana ◽  
Sheila González-Salvatierra ◽  
Manuel Muñoz-Torres ◽  
Beatriz García-Fontana
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Vascular Calcification ◽  
Computational Approach ◽  
Genetic Signature
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