Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 19 of 19 for “"structural alignment"”.
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Novel Algorithms for Structural Alignment of Non-coding RNAs
… tool for identifying and studying these structural RNAs, but also present some unique challenges for sequence analysis. Probabilistic covariance models are effective representations of structural RNAs, with generally high sensitivity and specificity but slow computational speed. New …
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Developmental trends in similarity as structural alignment: Evidence from children's performance in mapping tasks
"Young children find tasks in which object similarity is pitted against relational similarity difficult. However, there is a developmental improvement in the ability to use relational similarity. We investigated the effects of object similarity and relational similarity on children's performance in …
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Calculating the structure-based phylogenetic relationship of distantly related homologous proteins utilizing maximum likelihood structural alignment combinatorics and a novel structural molecular clock hypothesis
… this proposed methodology: a protein structure alignment program that proficiently superimposes distant homologs, an accurate structure-dependent sequence alignment program, and a dendrogram generation program that employs a novel structural molecular clock hypothesis. The results from this …
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Alignability and Prior Knowledge in Category Learning
This thesis is concerned with the roles of structural alignment and prior knowledge in category learning. Structural alignment (Gentner, 1983, 1989) is a theory that claims that similarity comparisons entail a process of aligning the components of the things being compared, determining what …
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Finding the commonalities: The role of analogical mapping during similarity judgments
… within a single framework. We suggest that structural alignment, like that proposed to mediate analogical reasoning, provides a sufficiently powerful process for determining the commonalities and differences of complex representations. In order to make this suggestion more concrete, we …
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Finding all maximal common substructures in proteins
… in drug and vaccine design. Unlikethe structural alignment problem, a good solution for the common substructureidentification problem should produce results that include:1. All possible common substructures (CS),2. CSs whose elements do not follow the same backbone order,3. CSs spanning …
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Biochemical and Structural Studies of Pseudouridine 55 Synthase
Sequence alignment of the families of PsiS identifies the conserved aspartic acid discussed previously as the strictly conserved amino acid. Structural alignment identifies the conserved tyrosine, which is part of hydrophobic core in the active site. The role of the conserved tyrosine is less …
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Protein Structure Analysis and Prediction
… of this study also suggest a new method for structural alignment using natural coordinates, and new evidence for long-range sequence patterns.
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Structural Analysis of Domain Swapping in the Protein Kinase: Crystal Structure of Human Ste20 OSR1 Kinase Domain
… cell motility. Moreover, from the viewpoint of structural biology, it is intriguing that the Ste20p family is characterized by the presence of a conserved kinase domain and a noncatalytic region of great diversity at various locations. Despite recent structural studies of Ste20p kinases such as …
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Analysis of a bacterial serine/threonine kinase
… superfamily. YihE however, bears the greatest structural similarity to choline kinase and aminoglycoside 3’-phosphotransferase [APH(3’)]-IIIa which are both atypical kinases. RdoA and YihE have demonstrated the capacity for autophosphorylation in vitro and the ability to phosphorylate myelin …
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Microfabrication Approaches for Understanding the Role of Vascular Mechanics in Progressive Diseases
… our technique, showing maintenance of patterned structural alignment and mechanical function over the course of two weeks. Lastly, we investigate the relationship between vascular disease and Alzheimer’s disease. Amyloid beta is a key precursor in the development of Alzheimer’s disease that …
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Real-Time Event Centric Data Integration
… qualitative spatial reasoning, fuzzy set and structural alignment similarities in order to define local similarity measures. Then we address the global similarity by treating the problem as a relational learning problem and use machine learning to learn the weights of each local similarity. To …
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Structural Self-Supervised Objectives for Transformers
… self-supervised pre-training tasks that exhibit structural alignment with downstream applications, leading to improved performance and reduced reliance on labeled data to achieve comparable results. We exploit the weak supervision provided by large corpora like Wikipedia and CC-News, challenging …
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Structural study of ExsA, the regulator of Type III Secretion System of Pseudomonas aeruginosa
… a combination of molecular biology tools and structural biology methods, we solved the N-terminal domain structure of the ExsA protein in P. aeruginosa. The model of the ExsA N-terminal domain has enriched our knowledge about ExsA dimerization and can serve as the base for mapping the …
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Protein structure prediction and structure-based protein function annotation
… structures are often conserved and hence protein structural similarity usually provide more clues on evolution of functionally related proteins. In this dissertation, I study the design of three bioinformatics modules that form a new hierarchical approach for structure prediction and function …
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Improved Algorithms for Alignment between RNA Tertiary Structures
… attention recently. It is a well known fact that structural features of RNAs are among the most significant factors in the molecular mechanisms involved in their functions. The presumption is that, to a preserved biological function there corresponds a preserved molecular structure. Therefore, the …
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The Influence of Structure and Surface Biochemistry on Cell Function and Angiogenesis in Collagen Scaffolds
… cell culture models, to study the effects of structural features and surface chemistry properties on the formation of microvessels. Firstly, the influence of mould design on architectural features of collagen scaffolds fabricated using lyophilisation was assessed using micro-computed …
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Improvement of the Capripoxvirus, lumpy skin disease virus for use as a vaccine vector
… homologue gene is truncated in nLSDV. Protein structural alignment of SOD homologues from LSDV and other characterised SOD homologues was done. Both the truncated and full-length SOD homologues lacked the catalytic arginine at position 142 which is involved in SOD activity. Some similarities …
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Characterizing the anti-angiogenic resistance potential of cross-family PDGF:VEGFR2 interactions in glioblastoma
Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01