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Relevant bibliographies by topics / Protein Structure Models

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Dissertations / Theses

Academic literature on the topic 'Protein Structure Models'

Author: Grafiati

Published: 6 September 2023

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Dissertations / Theses on the topic "Protein Structure Models"

1

Simons, Kim T. "Deciphering the protein folding code : ab initio prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/9234.

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2

Griffiths-Jones, Samuel R. "Peptide models for protein beta-sheets." Thesis, University of Nottingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.364650.

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3

Wróblewska, Liliana. "Refinement of reduced protein models with all-atom force fields." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/26606.

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The goal of the following thesis research was to develop a systematic approach for the refinement of low-resolution protein models, as a part of the protein structure prediction procedure. Significant progress has been made in the field of protein structure prediction and the contemporary methods are able to assemble correct topology for a large fraction of protein domains. But such approximate models are often not detailed enough for some important applications, including studies of reaction mechanisms, functional annotation, drug design or virtual ligand screening. The development of a metho

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4

Gamalielsson, Jonas. "Models for Protein Structure Prediction by Evolutionary Algorithms." Thesis, University of Skövde, Department of Computer Science, 2001. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-623.

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<p>Evolutionary algorithms (EAs) have been shown to be competent at solving complex, multimodal optimisation problems in applications where the search space is large and badly understood. EAs are therefore among the most promising classes of algorithms for solving the Protein Structure Prediction Problem (PSPP). The PSPP is how to derive the 3D-structure of a protein given only its sequence of amino acids. This dissertation defines, evaluates and shows limitations of simplified models for solving the PSPP. These simplified models are off-lattice extensions to the lattice HP model which has bee

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5

Käll, Lukas. "Predicting transmembrane topology and signal peptides with hidden Markov models /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-719-7/.

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6

Tångrot, Jeanette. "Structural Information and Hidden Markov Models for Biological Sequence Analysis." Doctoral thesis, Umeå universitet, Institutionen för datavetenskap, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1629.

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Bioinformatics is a fast-developing field, which makes use of computational methods to analyse and structure biological data. An important branch of bioinformatics is structure and function prediction of proteins, which is often based on finding relationships to already characterized proteins. It is known that two proteins with very similar sequences also share the same 3D structure. However, there are many proteins with similar structures that have no clear sequence similarity, which make it difficult to find these relationships. In this thesis, two methods for annotating protein domains are

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7

Pettitt, Christopher Steven. "Refinement of protein structure models with multi-objective genetic algorithms." Thesis, University College London (University of London), 2007. http://discovery.ucl.ac.uk/1446043/.

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Here I investigate the protein structure refinement problem for homology-based protein structure models. The refinement problem has been identified as a major bottleneck in the structure prediction process and inhibits the goal of producing high-resolution experimental quality structures for target protein sequences. This thesis is composed of three investigations into aspects of template-based modelling and refinement. In the primary investigation, empirical evidence is provided to support the hypothesis that using multiple template-based structures to model a target sequence can improve the

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8

Hayward, Steven John. "Studies in protein secondary structure prediction with neural network models." Thesis, University of Edinburgh, 1991. http://hdl.handle.net/1842/14034.

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The aim of this work was to predict protein secondary structure using neural network models. Initially a Hopfield network was used but abandoned in favour of a layered network trained using the back propagation algorithm. In the early stages of this work an exploration of the many different approaches to this problem was undertaken. These included attempts to predict boundaries between secondary structures, the secondary structures of individual residues, and the secondary structures of sequences wholly within a particular secondary structure. Results indicated the latter to be the best approa

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9

Gregor, Craig Robert. "Epitopes, aggregation and membrane binding : investigating the protein structure-function relationship." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/5833.

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The three-dimensional structure of a protein, formed as a result of amino-acid sequences folding into compact domains, is regarded as a key factor in its biological function. How and why proteins fold into specific topologies, remain the key focus of scientific research in the field of biophysics. By stripping down complex reactions down to the most basic elements, biophysicists aim to develop simplified models for biological phenomena such as antibody discrimination, viral fusion or self-assembly. Focusing on small model peptide systems, rather than the full proteins from which they were deri

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10

Chippington-Derrick, T. C. "Models, methods and algorithms for constraint dynamics simulations of long chain molecules." Thesis, University of Reading, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234776.

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