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Relevant bibliographies by topics / Protein sequence evolution

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Dissertations / Theses

Academic literature on the topic 'Protein sequence evolution'

Author: Grafiati

Published: 14 March 2023

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Dissertations / Theses on the topic "Protein sequence evolution"

1

Hollich, Volker. "Orthology and protein domain architecture evolution /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-783-9/.

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2

Kosiol, Carolin. "Markov models for protein sequence evolution." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614166.

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3

Warnecke, Tobias. "Determinants of coding sequence evolution- beyong protein function." Thesis, University of Bath, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531341.

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4

Guney, Tacettin Dogacan. "Prediction Of Protein-protein Interactions From Sequence Using Evolutionary Relations Of Proteins And Species." Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/12611058/index.pdf.

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Prediction of protein-protein interactions is an important part in understanding the biological processes in a living cell. There are completely sequenced organisms that do not yet have experimentally verified protein-protein interaction networks. For such organisms, we can not generally use a supervised method, where a portion of the protein-protein interaction network is used as training set. Furthermore, for newly-sequenced organisms, many other data sources, such as gene expression data and gene ontology annotations, that are used to identify protein-protein interaction networks may not be

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5

Davies, L. "Sequence database searching using structural models of protein evolution." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598371.

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Commonly used programs to search sequence databases such as BLAST, FASTA and SSEARCH identify sequence homology through pairwise alignment techniques. These programs are good at detecting closely related sequences but have problems accurately detecting homologous sequences with low sequence identity. This thesis describes a new approach that attempts to improve the detection of distantly related sequences by rejecting the assumption that all sites in a protein behave in an identical manner. This is done without the use of profile techniques, which require the preliminary collection of a set of

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6

Wistrand, Markus. "Hidden Markov models for remote protein homology detection /." Stockholm, 2005. http://diss.kib.ki.se/2006/91-7140-598-4/.

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7

Nordesjö, Olle. "Searching for novel protein-protein specificities using a combined approach of sequence co-evolution and local structural equilibration." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-275040.

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Greater understanding of how we can use protein simulations and statistical characteristics of biomolecular interfaces as proxies for biological function will make manifest major advances in protein engineering. Here we show how to use calculated change in binding affinity and coevolutionary scores to predict the functional effect of mutations in the interface between a Histidine Kinase and a Response Regulator. These proteins participate in the Two-Component Regulatory system, a system for intracellular signalling found in bacteria. We find that both scores work as proxies for functional muta

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8

Höglund, Pär J. "Identification, Characterization and Evolution of Membrane-bound Proteins /." Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9329.

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9

Dubey, Anshul. "Search and Analysis of the Sequence Space of a Protein Using Computational Tools." Diss., Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/14115.

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A new approach to the process of Directed Evolution is proposed, which utilizes different machine learning algorithms. Directed Evolution is a process of improving a protein for catalytic purposes by introducing random mutations in its sequence to create variants. Through these mutations, Directed Evolution explores the sequence space, which is defined as all the possible sequences for a given number of amino acids. Each variant sequence is divided into one of two classes, positive or negative, according to their activity or stability. By employing machine learning algorithms for feature selec

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10

Randall, Ryan Nicole. "Experimental phylogenetics: a benchmark for ancestral sequence reconstruction." Thesis, Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/48998.

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The field of molecular evolution has benefited greatly from the use of ancestral sequence reconstruction as a methodology to better understand the molecular mechanisms associated with functional divergence. The method of ancestral sequence reconstruction has never been experimentally validated despite the method being exploited to generate high profile publications and gaining wider use in many laboratories. The failure to validate such a method is a consequence of 1) our inability to travel back in time to document evolutionary transitions and 2) the slow pace of natural evolutionary processe

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