Relevant bibliographies by topics / Protein Structure Models / Dissertations / Theses
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Dissertations / Theses on the topic 'Protein Structure Models'

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Published: 6 September 2023

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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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11

Sidiqi, Mahjooba. "The structure and RNA-binding of poly (C) protein 1." University of Western Australia. School of Biomedical, Biomolecular and Chemical Sciences, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0077.

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[Truncated abstract] Regulation of mRNA stability is an important posttranscriptional mechanism involved in the control of gene expression. The rate of mRNA decay can differ greatly from one mRNA to another and may be regulated by RNA-protein interactions. A key determinant of mRNA decay are sequence instability (cis) elements often located in the 3' untranslated region (UTR) of many mRNAs. For example, the AU rich elements (AREs), are such well characterized elements, and most commonly involved in promoting mRNA degradation, and specific binding of proteins to these elements leading to the st
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12

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

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Thesis (Ph.D)--Biology, Georgia Institute of Technology, 2008.<br>Committee Chair: Skolnick, Jeffrey; Committee Member: Fernandez, Facundo; Committee Member: Jordan, King; Committee Member: McDonald, John; Committee Member: Sherrill, David. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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13

Aydin, Zafer. "Bayesian models and algoritms for protein secondary structure and beta-sheet prediction." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26471.

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Thesis (Ph.D)--Electrical and Computer Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Yucel Altunbasak; Committee Co-Chair: Mark Borodovsky; Committee Member: Brani Vidakovic; Committee Member: Ghassan Alregib; Committee Member: James McClellan; Committee Member: Russel Mersereau. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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14

Pontiggia, Francesco. "Protein structure and functionally-oriented dynamics: from atomistic to Coarse-grained models." Doctoral thesis, SISSA, 2008. http://hdl.handle.net/20.500.11767/3979.

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The overwhelming majority of biological processes relies on the capability of proteins to sustain conformational changes so to selectively recognise, bind and process other molecules, being them proteins, nucleic acids or other chemical compounds. The paradigmatic tripartite characterization of proteins in terms of sequence→structure→function has served to interpret the above-mentioned capability as being encoded in proteins' native structures, which is in turn determined by the amino acidic sequence...
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15

Tsilo, Lipontseng Cecilia. "Protein secondary structure prediction using neural networks and support vector machines." Thesis, Rhodes University, 2009. http://hdl.handle.net/10962/d1002809.

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Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), a
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16

Brown, Jennifer Louise. "Investigation of the molecular interactions between an anti-peptide antibody and its ligand." Thesis, University of Southampton, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318221.

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17

TUBB, MATTHEW ROBERT. "Apolipoprotein A-IV Structural Models and Functional Implications." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1218826062.

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18

Kurtz, Katryn Lucille. "Structure of chromatin, protein transitions, and post-translational histone modifications in several sperm models." Doctoral thesis, Universitat de Barcelona, 2008. http://hdl.handle.net/10803/1158.

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The study of chromatin structure in several simple sperm models of increasing complexity was performed. Species demonstrating different types of sperm nuclear protein transitions and structural changes in spermatic chromatin during spermiogenesis were selected as models for comparison: "H" (non-histone proteins are removed), "H->P" (protamine displaces histones), and "H->Pp->P" (precursor protamine displaces histones, and subsequently is converted into the mature protamine). This study has an evolutionary focus, in which a primitive sperm model is identified, from which more complex models may
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19

Gough, J. "Hidden Markov models and their application to genome analysis in the context of protein structure." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599547.

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The bulk of the thesis is concerned with the application of hidden Markov models (HMMs) to remote protein homology detection. The thesis both addresses how best to utilise HMMs, and then uses them to analyse all completely sequenced genomes. There is a structural perspective to the work, and a section on three-dimensional protein structure analysis is included. The Structural Classification of Proteins (SCOP) database forms the basis of the structural perspective. SCOP is a hierarchical database of protein domains classified by their structure, sequence and function. The main aim of the work i
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20

Murray, Ian V. J. "Acylation stimulating protein (ASP) structure & function studies : in vitro and in vivo in mouse models." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ55363.pdf.

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21

Kim, Seoung Bum. "Data Mining in Tree-Based Models and Large-Scale Contingency Tables." Diss., Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/6825.

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This thesis is composed of two parts. The first part pertains to tree-based models. The second part deals with multiple testing in large-scale contingency tables. Tree-based models have gained enormous popularity in statistical modeling and data mining. We propose a novel tree-pruning algorithm called frontier-based tree-pruning algorithm (FBP). The new method has an order of computational complexity comparable to cost-complexity pruning (CCP). Regarding tree pruning, it provides a full spectrum of information. Numerical study on real data sets reveals a surprise: in the complexity-penalizatio
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22

Planas, Iglesias Joan 1980. "On the study of 3D structure of proteins for developing new algorithms to complete the interactome and cell signalling networks." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/104152.

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Proteins are indispensable players in virtually all biological events. The functions of proteins are determined by their three dimensional (3D) structure and coordinated through intricate networks of protein-protein interactions (PPIs). Hence, a deep comprehension of such networks turns out to be crucial for understanding the cellular biology. Computational approaches have become critical tools for analysing PPI networks. In silico methods take advantage of the existing PPI knowledge to both predict new interactions and predict the function of proteins. Regarding the task of predicting PPIs, s
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23

Mishra, Avdesh. "Effective Statistical Energy Function Based Protein Un/Structure Prediction." ScholarWorks@UNO, 2019. https://scholarworks.uno.edu/td/2674.

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Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D
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24

Glidden, Michael D. II. "Single-chain insulin analogs as ultra-stable therapeutics and as models of protein (mis)folding: stability, structure, dynamics, and function of novel analogs." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1522270994798884.

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25

Hudson, Cody Landon. "Protein structure analysis and prediction utilizing the Fuzzy Greedy K-means Decision Forest model and Hierarchically-Clustered Hidden Markov Models method." Thesis, University of Central Arkansas, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1549796.

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<p>Structural genomics is a field of study that strives to derive and analyze the structural characteristics of proteins through means of experimentation and prediction using software and other automatic processes. Alongside implications for more effective drug design, the main motivation for structural genomics concerns the elucidation of each protein&rsquo;s function, given that the structure of a protein almost completely governs its function. Historically, the approach to derive the structure of a protein has been through exceedingly expensive, complex, and time consuming methods such as x
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26

Robertson, Timothy Allen. "Development and validation of statistical potential functions for the prediction of protein/nucleic-acid interactions from structure /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9268.

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27

Cheng, Haitao. "Protein structure prediction and conformational transitions I. Improvement of protein secondary structure prediction : II. Pathways of conformational transition originating in phosphorylation : a study of CDK2 using targeted molecular dynamics and coarse grained models /." [Ames, Iowa : Iowa State University], 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3360333.

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28

Hägglöf, Peter. "Plasminogen activator inhibitor type-1 : structure-function studies and its use as a reference for intramolecular distance measurements /." Umeå : Umeå University, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-177.

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29

Brewer, Allan Ronald. "Computational protein structure prediction using physico-chemical force fields : assessing reduced-atom and torsional models for accelerating the phase-space search process." Thesis, University of Bristol, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.427889.

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30

Tetley, Romain. "Analyse mixte de protéines basée sur la séquence et la structure - applications à l'annotation fonctionnelle." Thesis, Université Côte d'Azur (ComUE), 2018. http://www.theses.fr/2018AZUR4111/document.

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Dans cette thèse, l'emphase est mise sur la réconciliation de l'analyse de structure et de séquence pour les protéines. L'analyse de séquence brille lorsqu'il s'agit de comparer des protéines présentant une forte identité de séquence (≤ 30\%) mais laisse à désirer pour identifier des homologues lointains. L'analyse de structure est une alternative intéressante. Cependant, les méthodes de résolution de structures sont coûteuses et complexes - lorsque toutefois elles produisent des résultats. Ces observations rendent évident la nécessité de développer des méthodes hybrides, exploitant l'informat
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31

Dressel, Frank. "Sequenz, Energie, Struktur - Untersuchungen zur Beziehung zwischen Primär- und Tertiärstruktur in globulären und Membran-Proteinen." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1222781322751-68621.

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Proteine spielen auf der zellulären Ebene eines Organismus eine fundamentale Rolle. Sie sind quasi die „Maschinen“ der Zelle. Ihre Bedeutung wird nicht zuletzt in ihrem Namen deutlich, welcher 1838 erstmals von J. Berzelius verwendet wurde und „das Erste“, „das Wichtigste“ bedeutet. Proteine sind aus Aminosäuren aufgebaute Moleküle. Unter physiologischen Bedingungen besitzen sie eine definierte dreidimensionale Gestalt, welche für ihre biologische Funktion bestimmend ist. Es wird heutzutage davon ausgegangen, dass diese dreidimensionale, stabile Struktur von Proteinen eindeutig durch die Abfol
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32

Frouws, Timothy Duncan. "Iterative helical real-space reconstruction of histone octamer tubular crystals and implications for the 30 nm chromatin fiber." Thesis, University of the Western Cape, 2006. http://etd.uwc.ac.za/index.php?module=etd&amp.

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33

Lubbe, Lizel. "Cloning and Expression of the M-Gene from the Human Coronavirus NL-63 in Different Expression Systems." Thesis, University of the Western Cape, 2008. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_2721_1266364969.

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<p>In this study, the HCoV-NL63 genome was transcribed from RNA to DNA from which the M gene was amplified with various primers designed for use in specific expression systems. The various genes were cloned into the pGEM vector and confirmed by sequencing. The genes were now expressed in cloning vectors suited for each expression system (pFastBac for baculovirus expression, pFlexi for bacterial expression and pCMV for mammalian expression). Clones were sequenced for a second time. The recombinant clone in pFlexi was expressed in KRX cells and a 36hr time course was performed. The recombinant p
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34

Nordling, Erik. "Biocomputational studies on protein structures /." Stockholm, 2002.

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35

Chen, Yiwen Superfine Richard. "Probing protein structural dynamics using simplified models." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,1093.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.<br>Title from electronic title page (viewed Mar. 27, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Physics and Astronomy." Discipline: Physics and Astronomy; Department/School: Physics and Astronomy.
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36

Uziela, Karolis. "Protein Model Quality Assessment : A Machine Learning Approach." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-137695.

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Many protein structure prediction programs exist and they can efficiently generate a number of protein models of a varying quality. One of the problems is that it is difficult to know which model is the best one for a given target sequence. Selecting the best model is one of the major tasks of Model Quality Assessment Programs (MQAPs). These programs are able to predict model accuracy before the native structure is determined. The accuracy estimation can be divided into two parts: global (the whole model accuracy) and local (the accuracy of each residue). ProQ2 is one of the most successful MQ
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37

Silva, Aparecido Rodrigues da. "Desenvolvimento e avaliação de modelos representativos para construção de aminoácidos e de estruturas de proteínas." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/76/76132/tde-16022011-091415/.

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Foi desenvolvido um conjunto de peças plásticas que permitem a montagem e representação dos aminoácidos mais comuns, bem como a construção de estruturas protéicas. Durante e após o desenvolvimento o material foi submetido a várias etapas de avaliação por professores (do ensino básico e universitário), alunos de pós-graduação e de graduação. A primeira etapa foi o desenvolvimento dos modelos em ambiente computacional, seguida da prototipagem das peças. Após discussão com a comunidade científica (apresentados na XXXVI Reunião Anual da SBBq em 2007) as sugestões foram implementadas nos modelos co
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38

Wallner, Björn. "Protein Structure Prediction : Model Building and Quality Assessment." Doctoral thesis, Stockholm University, Department of Biochemistry and Biophysics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-649.

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<p>Proteins play a crucial roll in all biological processes. The wide range of protein functions is made possible through the many different conformations that the protein chain can adopt. The structure of a protein is extremely important for its function, but to determine the structure of protein experimentally is both difficult and time consuming. In fact with the current methods it is not possible to study all the billions of proteins in the world by experiments. Hence, for the vast majority of proteins the only way to get structural information is through the use of a method that predicts
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39

Wallner, Björn. "Protein structure prediction : model building and quality assessment /." Stockholm : Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-649.

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40

SUBRAMANIAN, SUCHITHA. "PROTEIN STRUCTURE ALIGNMENT USING A GENERALIZED ALIGNMENT MODEL." University of Cincinnati / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1191966691.

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41

Trovato, Antonio. "A Geometric perspective on protein structures and heteropolymer models." Doctoral thesis, SISSA, 2000. http://hdl.handle.net/20.500.11767/3962.

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42

Polozov, Ivan V. "Interactions of class A and class L amphipathic helical peptides with model membranes." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0006/NQ30110.pdf.

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43

Davies, Lisa Joy. "Structural models of protein evolution in database searching." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.620508.

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44

Blackburne, Benjamin P. "Functional model proteins : structure, function and evolution." Thesis, University of Nottingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.405144.

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45

Le, Treut Guillaume. "Models of chromosome architecture and connection with the regulation of genetic expression." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS411/document.

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Plusieurs indices suggèrent que le repliement du chromosome et la régulation de l’expression génétique sont étroitement liés. Par exemple, la co-expression d’un grand nombre de gènes est favorisée par leur rapprochement dans l’espace cellulaire. En outre, le repliement du chromosome permet de faire émerger des structures fonctionnelles. Celles-ci peuvent être des amas condensés et fibrillaires, interdisant l’accès à l’ADN, ou au contraire des configurations plus ouvertes de l’ADN avec quelques amas globulaires, comme c’est le cas avec les usines de transcription. Bien que dissemblables au prem
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46

Lutya, Portia Thandokazi. "Expression and purification of the novel protein domain DWNN." Thesis, University of the Western Cape, 2002. http://etd.uwc.ac.za/index.php?module=etd&amp.

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Proteins play an important role in cells, as the morphology, function and activities of the cell depend on the proteins they express. The key to understanding how different proteins function lies in an understanding of the molecular structure. The overall aim of this thesis was the determination of the structure of DWNN domains. This thesis described the preparation of samples of human DWNN suitable for structural analysis by nuclear magnetic resonance spectroscopy (NMR), as well as NMR analysis.
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47

Fraga, Keith Jeffrey. "Explorations into protein structure with the knob-socket model." Scholarly Commons, 2016. https://scholarlycommons.pacific.edu/uop_etds/264.

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Protein sequences contain the information in order for a protein to fold to a unique compact, three-dimensional native structure. The forces that drive protein structures to form compact folds are largely dominated by burial of hydrophobic amino acids, which results in non-specific packing of amino acid side-chains. The knob-socket model attempts to organize side-chain packing into tetrahedral packing motifs. This tetrahedral motif is characterized with a three residues on the same secondary structure forming the base of the tetrahedron packing with a side-chain from a separate secondary struc
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48

Tanley, Simon. "Structural chemistry and structural biology of anti-cancer agents binding to proteins with reference to a model protein and to heparanase." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/structural-chemistry-and-structural-biology-of-anticancer-agents-binding-to-proteins-with-reference-to-a-model-protein-and-to-heparanase(b14a04ea-d7db-4846-a717-84d013478698).html.

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The binding of cisplatin and carboplatin to hen egg white lysozyme, a model protein, has been studied using X-ray crystallography under many different crystallisation conditions (Tanley et al, 2012a; 2012b; 2013a; 2013b and Helliwell & Tanley, 2013). From this work, many new results have been obtained; (1) Two molecules of cisplatin and carboplatin are bound to HEWL in DMSO media using the co-crystallisation method. (2) Two molecules of cisplatin are bound to HEWL in aqueous media after a prolonged chemical exposure of 13months. (3) Cisplatin is stable up to 1.78MGy of X-ray radiation when bou
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49

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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50

Carlsson, Jonas. "Mutational effects on protein structure and function." Doctoral thesis, Linköpings universitet, Bioinformatik, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-50491.

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In this thesis several important proteins are investigated from a structural perspective. Some of the proteins are disease related while other have important but not completely characterised functions. The techniques used are general as demonstrated by applications on metabolic proteins (CYP21, CYP11B1, IAPP, ADH3), regulatory proteins (p53, GDNF) and a transporter protein (ANTR1). When the protein CYP21 (steroid 21-hydroxylase) is deficient it causes CAH (congenital adrenal hyperplasia). For this protein, there are about 60 known mutations with characterised clinical phenotypes. Using manual
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