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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 48 for “"Protein structure prediction"”.
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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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Inference Time Search for Protein Structure Prediction
… not yet been made in the field of biomolecular structure prediction. We introduce a new paradigm for inference-time search by adding architectural components and a finetuning procedure to state-of-the-art structure prediction models that give rise to a discrete latent space. We implement …
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An analysis of representations for protein structure prediction
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1994.
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Protein structure prediction and structure-based protein function annotation
… tends to modify rather than invent function of protein molecules, and the log of the modifications is encrypted in the gene sequence. Analysis of these modification events in evolutionarily related genes is important for assigning function to hypothetical genes and their products surging in …
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Application of the Statistical Energy Landscape Theory to Protein Structure Prediction
… much slower rate. Consequently, the sequence to structure gap is still growing. Many scientists are looking to structure prediction through computational methods to narrow this gap. Using ideas from the energy landscape theory first introduced by Bryngelson and Wolynes, and database analysis, we …
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Interpretable and controllable Statistical Inference Models for Protein Structure Prediction and Sequence Design
L'abstract è presente nell'allegato / the abstract is in the attachment
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Change of representation in machine learning, and an application to protein structure prediction
… induction algorithms are known for making predictions from databases in well-studied domains, learning systems still perform poorly in many difficult real-world domains, such as weather prediction or financial risk analysis. Two characteristics of real-world domains are inadequately …
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The Energy Landscape of Associative Memory Energy Functions and Their Application to Ab Initio Protein Structure Prediction
The ability to predict the structure of a protein from its amino acid sequence is one of the major practical benefits that it is hoped will result from a greater understanding of the physics of protein folding. For sequences for which a highly homologous sequence with known structure is available, …
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Development of Models for the Action of Novel Anti-apoptotic Proteins using Gene Regulation, Pathway Analysis and Protein Structure Prediction
… study also sought to characterise the predicted structures of some of the key proteins that regulate these pathways and networks. The wider aim of the work was to use these bioinformatics approaches to underpin and facilitate future efforts at designing novel anti-cancer drugs for ovarian and …
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Theoretical and computational studies of bio-molecular systems : structure and dynamics
… in this thesis is relevant for the study of structure, function and dynamics of complex bio-molecular systems. The thesis contains two parts related to (1) protein structure prediction, and (2) free energy profile calculations in nano-scale systems. The new contributions reported in this …
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A Novel Statistical Potential for Protein Beta-Sheets Prediction
… computational scientists and experimentalists is protein structure prediction, whose goal is to obtain three-dimensional native protein structure from one-dimensional sequence. In protein structure prediction problems, a fundamental problem is Beta-sheets structure prediction. Though more than 85% …
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Protein Structure Analysis and Prediction
The protein structure prediction problem consists of three separate subproblems: modeling the protein structure, modeling the protein energetics, and the problem of searching for low-energy structures in high-dimensional space in the presence of many local minima. This study presents a new approach …
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Predicting protein residue-residue contacts and disorder
… OF MISSOURI AT AUTHOR'S REQUEST.] Predicting a protein's three dimensional structure from its corresponding sequence has long been an extremely important and challenging problem in the field of Structural Bioinformatics. A principle difficulty has been in efficiently exploring the large number …
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Efficient algorithm for selecting protein residue-residue contacts
"The functions of proteins are largely determined by their structures. Determination of the protein three-dimensional structure is experimentally and computationally challenging. Since amino acids residues that are spatially close often co-evolve, the correlation allows us to predict the contacts …
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ChaperoNet: Distillation of Language Model Semantics to Folded Three-Dimensional Protein Structures
Determining the structure of proteins has been a long-standing goal in biology. Lan- guage models have been recently deployed to capture the evolutionary semantics of protein sequences, and as an emergent property, were found to be structural learn- ers. Enriched with multiple sequence alignments …
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Machine Learning Methods for Protein Model Quality Estimation
In my research, I developed protein model quality estimation methods aimed at evaluating the reliability of computationally predicted protein models in the absence of experimentally solved ground truth structures. These methods specifically focus on estimating errors within the protein models to …
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Modeling Biomolecular Interactions with Generative Models
… AlphaFold2 revolutionized single-chain protein structure prediction achieving atomic accuracy, solving a longstanding challenge in biology. However, understanding biomolecular interactions, a critical problem for advancing drug discovery and biological research, remained unsolved. This …
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State-of-the-art Approaches for Sequencing, Assembling and Annotating Naphthenic Acid Degrading Bacterial Metagenomes
… putative phages. I also include state-of-the-art protein structure prediction and structure homology search tools, which greatly enrich annotations of novel sequences that are below the threshold for homology finding by sequence alone. Overall, these approaches unveiled a diverse and constantly …
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Deep learning and coevolution reveal proteome-wide protein-protein interactions
The total set of potential protein-protein interactions (PPI) within an organism's proteome guides a plethora of potential biological processes at an organism’s disposal. Understanding these PPIs is critical to our understanding of biological systems, however identifying interactions with high …
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