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 20 of 433 for “"secondary structure"”.
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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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Advanced tools for RNA secondary structure analysis
The analysis of RNA secondary structure has become more and more important throughout the last decades after it was recognised that RNA does not only serve as a passive messenger (mRNA), but also as a functional compound of the cell. Furthermore, it was elucidated that mainly the structure rather …
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Enhancing RNA Foundation Models via Secondary Structure Modelling
… by its functional dependence on complex structure. Modelling this intricate sequence-structure-function relationship represents a vital problem in computational biology. This thesis aims to resolve three core impediments to progress in structure-aware RNA Foundation Model (FM). First, the …
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Protein secondary structure mimetics : design, synthesis and evaluation
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1996.
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DNA Secondary Structure in Human Disease and Gene Regulation
DNA secondary structures have critical roles in normal cellular processes and human diseases, but the extent of their formation and regulation on a genome-wide level is still not fully understood. The goal of this work is to further explore the role of DNA secondary structure formation in human …
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Flexible protein annotation with sequence- and secondary structure information
Eine Standardproblem der Sequenzanalyse in der Bioinformatik ist die Verwandtschaftssuche, bei der eine Datenbank nach verwandten Genen zu einer Anfragesequenz durchsucht wird. Obwohl es hierfür bereits verschiedene Ansätze gibt, ist noch Raum für Erweiterungen vorhanden. Eine Möglichkeit ist es, …
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Tertiary packing effects on secondary structure formation in proteins
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1996.
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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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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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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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Structural and Functional Analysis of Secondary Structure Block to mRNA Utilization
<p>Experimentally introduced secondary structure, formed by a cis-targeted hammerhead ribozyme in exon 2 two nucleotides dowstream of the 3' splice site of a yeast ACT-E. <em>coli lacZ fusion</em> gene, virtually abolishes splicing in vivo and inhibits B-galactosidase production. This is the first …
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A multi-level nearest-neighbour algorithm for predicting protein secondary structure
… on machine learning and prediction of protein secondary structure. We develop a variation of the nearest-neighbour algorithm that adopts a multi-level strategy together with a variable window size. The algorithm is applied to the problem of predicting the secondary structure of a protein given …
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Design evaluation of naval combatant secondary structure under hydrostatic lateral load
Thesis (S.M. in Naval Architecture and Marine Engineering)--Massachusetts Institute of Technology, Dept. of Ocean Engineering; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2003.
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Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency
… signatures that characterize equilibrium secondary structure of the participating mRNA, siRNA, and their complexes. A previously published data set of 609 experimental points was used for the analysis. While virtually no correlation with the computed structural signatures are observed for …
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Performance analysis of a reduced cost manufacturing process for composite aircraft secondary structure
… the performance of<br/>carbon fibre sandwich secondary structure that are manufactured using several different<br/>techniques. Cost and performance criteria are defined so that an optimal panel can be produced.<br/>The work has been motivated by the industrial sponsor, GE Aviation Systems. …
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Natural selection on MRNA secondary structure and its correlation with protein functional groups
… to investigate whether the stability of the secondary structures of mRNAs has been the subject of natural selection. The DNA sequence that codes for a particular target protein is only partially determined by that protein, since the redundancy of the genetic code permits multiple possible …
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Computational Development for Secondary Structure Detection From Three-Dimensional Images of Cryo-Electron Microscopy
… from three-dimensional (3D) density images, secondary structure elements (SSEs) such as alpha-helices and beta-sheets can still be detected. The accuracy of SSE detection from the volumetric protein density images is critical for <em>ab initio</em> backbone structure derivation in cryo-EM. So …
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Molecular Comparisons of Colicin Ia and Colicin Ib (Dna Sequence, Secondary Structure, Immunity Genes)
Colicin Ia and colicin Ib have three distinct functional characteristics, receptor specificity, mode of action and immunity recognition. Both colicins bind to the same receptor and kill sensitive Escherichia coli cells by depolarizing the cell membrane. Sensitive cells carrying the colicin Ib …
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Exploring induced secondary structure and unmethylated DNA binding domains of methyl CpG binding protein 2 (MeCP2)
… of Methyl CpG binding protein 2 (MeCP2) structure and function has changed and expanded considerably over the last two decades. Mutations along the entirety of the human MeCP2 gene product lead to a disease state - Rett syndrome. The clinical connection of this protein has continued to …
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