Global ETD Search
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Showing 1 to 17 of 17 for “"secondary structure prediction"”.
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RNA secondary structure prediction using hybrid methods
… presents a novel two-stage framework for RNA secondary structure prediction, introducing deep learning models that address local substructure prediction and global structure assembly. Drawing insights from RNA folding kinetics, the stage-1 (S1) model proposes local substructures as pixel-level …
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Review of algorithms for RNA secondary structure prediction with pseudoknots
Pseudoknots are structures that are formed from the base pairing of an RNA secondary loop structure with a complementary base which lies somewhere outside of the loop. The result is a structure, which plays a vital role in cell structure rigidity, regulation of protein synthesis, and in the …
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Fast learning optimized prediction methodology for protein secondary structure prediction, relative solvent accessibility prediction and phosphorylation prediction
… the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number of structures. There is therefore an urgent need to develop computed structures and identify the functions of these …
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RNA secondary structure detection programs with an emphasis on covariance models
RNA secondary structure prediction requires a different approach from traditional alignment methods. Functional RNAs often have their secondary structure better conserved than their primary structure. Covariance models, probabilistic models that utilize stochastic-context-free grammars, are one …
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Diverse primary and secondary structural features are associated with Y complex-dependent mRNA maturation in B. subtilis
… sequence motif searches, kmer analysis and secondary structure prediction to analyze these 21 cleavage sites and their surrounding regions. We find enrichment for a guanine immediately preceding the cleavage site. Such enrichment has been previously observed in Staphylococcus aureus RNase Y …
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Protein structure prediction and conformational transitions
<p>There is a critical need for protein structure and function prediction. Accurate protein secondary structure prediction is essential for many bioinformatics applications, including protein tertiary structure prediction. We developed an algorithm (Fragment Data Mining, FDM) for protein secondary …
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DEVELOPMENT OF E-SRS (ENVIRONMENT-SENSING RESPONSE SYSTEM) AS A NOVEL METHOD TO DISTINGUISH GENETIC ENVIRONMENTS AND RESOLVE CLOSELY RELATED NUCLEIC ACID SEQUENCES
… RNA folding was designed without computational secondary structure prediction. The RNA folding likely did not occur as intended. We redesigned the physical implementation to create the current e-SRS, adapting an existing allosteric ribozyme, the Maxizyme, as e-SRS sensor, employing computational …
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Analysis of protein secondary structure via the discrete wavelet transform
<p>This project develops a secondary structure prediction approach that uses the discrete wavelet transform. In order to use the wavelet technique, we convert the primary amino acid sequence of the protein to a numerical signal using the hydrophobic tendencies associated with the amino acids. The …
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Molecular modelling of Androglobin
… motif. Here we will explore the molecular structure of Adgb. This will be achieved by first exposing the sequence to disorder prediction algorithms with the aims of identifying intrinsically disordered regions (IDRs), that may not only add noise when subjecting the sequence to fold …
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Midaesin - a histone H2A antimicrobial peptide from the South African abalone, Haliotis midae
… proportion of hydrophobic and basic residues. Secondary structure prediction of Midaesin revealed the presence of an amphipathic α-helix. Alignment of the Midaesin peptide to other known histone H2A-derived AMPs revealed significant sequence similarity. Additionally, RT-qPCR of total cDNA …
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The evolutionary impacts of secondary structures within genomes of eukaryote-infecting single-stranded DNA viruses
Secondary structures forming through base-pairing in virus genomes have been proven to regulate several processes during viral replication cycles, including genome replication, transcription, post-transcriptional activities, protein synthesis, genome packaging, generation of viral sub-genomes and …
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Recombinant expression, purification and structural characterization of aspergillus niger ring finger domain using nuclear magnetic resonance spectroscopy
… domain. Previous studies determined the solution structure of the human RING finger domain using heteronuclear NMR spectroscopy. A bioinformatics analysis using the human RING finger from RBBP6 as searching bait revealed an unchanged zinc ion coordination pattern in all organisms except in three …
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Transcriptome-wide pseudouridine profiling reveals modification of critical E. coli mRNAs
… In Chapter 1, I provide an overview of the structure and function of pseudouridine, focusing on the properties that can impact the structure, translation, and interactome of the mRNAs that contain it. I give a brief review of the enzymes that carry out tRNA and rRNA modification, which are …
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Structural Characterisation of the Mammalian SRP Receptor
… effector interactions should be obtained. X-ray structure analysis was used to determine the structure of a soluble form of SRβ (SRβΔTM) in its GTP bound state in complex with a fragment of SRα. The structure allows to precisely define the minimal SRβ binding domain of SRα (SRX). The homology to …
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Structural and biochemical analysis of the Y-shaped Nup84 subcomplex of the NPC
… interest and importance. Here, I investigate the structure and assembly of one of the major components of the NPC scaffold, the Nup84 complex. Also known as the Y complex, this 7- membered assembly adopts the shape of an extended Y in solution. We solved the structure of the heterodimeric Nup85 …
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Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes
… certain DNA and RNA virus genomes form complex secondary structures through Watson-Crick base-pairing interactions between bases on the same DNA or RNA strand. Both computational and experimental methods are available for determining the secondary structure conformations of nucleotide sequences …
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Structural and functional studies of sodium/dicarboxylate cotransporters
… based on hydropathy analysis, contains 11 TM but secondary structure prediction algorithms predict at least 13 TM. To differentiate between the 11 and the 13 TM models, individual cysteine residues were substituted for other amino acids in predicted extracellular and intracellular loops of …