Relevant bibliographies by topics / Computational Molecular Biology / Dissertations / Theses
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Dissertations / Theses on the topic 'Computational Molecular Biology'

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Published: 11 March 2023
Last updated: 31 July 2025

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1

Istrail, Sorin. "Computational molecular biology /." Amsterdam [u.a.] : Elsevier, 2003. http://www.loc.gov/catdir/toc/fy037/2003051360.html.

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2

Vialette, Stéphane. "Algorithmic Contributions to Computational Molecular Biology." Habilitation à diriger des recherches, Université Paris-Est, 2010. http://tel.archives-ouvertes.fr/tel-00862069.

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3

Pettersson, Fredrik. "A multivariate approach to computational molecular biology." Doctoral thesis, Umeå : Univ, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-609.

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4

Dinescu, Adriana. "Metals in Chemistry and Biology: Computational Chemistry Studies." Thesis, University of North Texas, 2007. https://digital.library.unt.edu/ark:/67531/metadc3678/.

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Numerous enzymatic reactions are controlled by the chemistry of metallic ions. This dissertation investigates the electronic properties of three transition metal (copper, chromium, and nickel) complexes and describes modeling studies performed on glutathione synthetase. (1) Copper nitrene complexes were computationally characterized, as these complexes have yet to be experimentally isolated. (2) Multireference calculations were carried out on a symmetric C2v chromium dimer derived from the crystal structure of the [(tBu3SiO)Cr(µ-OSitBu3)]2 complex. (3) The T-shaped geometry of a three-coordina
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5

Karathia, Hiren Mahendrabhai. "Development and application of computational methdologies for Integrated Molecular Systems Biology." Doctoral thesis, Universitat de Lleida, 2012. http://hdl.handle.net/10803/110518.

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L'objectiu del treball presentat en aquesta tesi va ser el desenvolupament i l'aplicació de metodologies computacionals que integren l’anàlisis de informació sobre seqüències proteiques, informació funcional i genòmica per a la reconstrucció, anotació i organització de proteomes complets, de manera que els resultats es poden comparar entre qualsevol nombre d'organismes amb genomes completament seqüenciats. Metodològicament, m'he centrat en la identificació de l'organització molecular dins d'un proteoma complet d'un organisme de referència i comparació amb proteomes d'altres organismes, en esp
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6

Donaldson, Eric F. Baric Ralph S. "Computational and molecular biology approaches to viral replication and pathogenesis." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,1731.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.<br>Title from electronic title page (viewed Sep. 16, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Microbiology and Immunology Virology." Discipline: Microbiology and Immunology; Department/School: Medicine.
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7

Cao, Dan. "Computational and experimental analysis of mRNA degradationin Saccharomyces cerevisiae." Diss., The University of Arizona, 2002. http://hdl.handle.net/10150/280160.

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Because of its integration power, quantifying power, explanatory power and predictive power, mathematical and computational modeling is becoming an important tool to test and advance our understanding about cellular process in the post-genomic era. Iterative approach between modeling, making prediction and experimental testing might increase the rate of forming and testing hypotheses in Biology. mRNA decay is an ideal system to start knowledge based modeling. In the second chapter, I applied the computational modeling approach to test our understanding about normal mRNA turnover processes in y
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8

Weis, Michael Christian. "Computational Models of the Mammalian Cell Cycle." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1323278159.

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9

Ensterö, Mats. "The multi-faceted RNA molecule : Characterization and Function in the regulation of Gene Expression." Doctoral thesis, Stockholm University, Department of Molecular Biology and Functional Genomics, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7729.

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<p>In this thesis I have studied the RNA molecule and its function and characteristics in the regulation of gene expression. I have focused on two events that are important for the regulation of the transcriptome: Translational regulation through micro RNAs; and RNA editing through adenosine deaminations.</p><p>Micro RNAs (miRNAs) are ~22 nucleotides long RNA molecules that by semi complementarity bind to untranslated regions of a target messenger RNA (mRNA). The interaction manifests through an RNA/protein complex and act mainly by repressing translation of the target mRNA. I have shown that
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10

Zwolak, Jason Walter. "Computational Tools for Molecular Networks in Biological Systems." Diss., Virginia Tech, 2004. http://hdl.handle.net/10919/30274.

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Theoretical molecular biologists try to understand the workings of cells through mathematics. Some theoreticians use systems of ordinary differential equations (ODEs) as the basis for mathematical modelling of molecular networks. This thesis develops algorithms for estimating molecular reaction rate constants within those mathematical models by fitting the models to experimental data. An additional step is taken to fit non-timecourse experimental data (e.g., transformations must be performed on the ODE solutions before the experimental and simulation data are similar, and therefore, compara
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11

Mitchell, Carter Alexander. "Structural, functional, and computational insights into the ANL superfamily of enzymes." Thesis, State University of New York at Buffalo, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3598714.

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<p> Members of the ANL superfamily of enzymes are involved in primary and secondary metabolism throughout all domains of life and identify key pathways that contribute to essential physiological reactions as well as defense mechanisms to evade competition. Specifically, acetyl-CoA synthetases are directly involved in energy metabolism, while NonRibosoaml Peptide Synthetases and some Aryl-CoA Ligases produce secondary natural products that confer virulence for the producing organism. Due to the ANL superfamily's ubiquitous involvement in primary and secondary metabolism, gaining an understandin
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12

Romagnoli, Dario. "Identification and development of epigenetic tumor biomarkers through computational biology approaches." Doctoral thesis, Università di Siena, 2023. https://hdl.handle.net/11365/1227695.

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DNA-methylation alterations are common in cancer and display unique characteristics that make them ideal markers for tumor quantification and classification. In this study, we discuss the development and testing of a computational framework exploiting minimal DNA-methylation signatures composed by a few dozen informative DNA-methylation sites to quantify and classify tumor signals in tissue and cell-free DNA samples. Extensive analyses of multiple independent and heterogenous datasets including &gt;7,200 samples demonstrate the capability of the framework to provide precise estimations of tumo
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13

Redij, Tejashree. "Rational Design of Anti-diabetic Agents." Thesis, University of the Sciences in Philadelphia, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=13861629.

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<p> The Glucagon-like peptide 1 receptor (GLP-1R) belongs to the pharmaceutically important Class B family of G-protein coupled receptors (GPCRs) and its incretin peptide ligand GLP-1 analogs are adopted drugs for the treatment of type 2 diabetes (T2D). Despite remarkable anti-diabetic effects, Glucagon Like Peptide-1 (GLP-1) peptide-based drugs are limited by the need of injection or high cost oral formulation. On the other hand, developing non-peptide small molecule drugs targeting GLP-1R remains elusive likely due to the large nature of the orthosteric binding site on GLP-1R. A promising ap
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14

Octavio, Leah M. (Leah Mae Manalo). "Molecular systems analysis of a cis-encoded epigenetic switch." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/68433.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>An ability to control the degree of heterogeneity in cellular phenotypes may be important for cell populations to survive uncertain and ever-changing environments or make cell-fate decisions in response to external stimuli. Cells may control the degree of gene expression heterogeneity and ultimately levels of phenotypic heterogeneity by modulating promoter switching dynamics. In this thesis, I investigated v
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15

Ghule, S. "Computational development of the strategies to explore molecular machines and the molecular space for desired properties using machine learning." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2022. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/6165.

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Ph. D. Thesis of Siddharth Ghule Division: Physical and Material Chemistry NCL-ID No.: 11865 AcSIR Roll No.: 10CC17A26010 Name of research Guide/co-guide: Dr. Kumar Vanka Names of DAC Members: Paresh Laxmikant Dhepe, Kavita Joshi, Nayana Vaval Date of joining NCL: 24-07-2017 Faculty: Chemical Sciences<br>For thousands of years, scientific discoveries have played a vital role in the progress of human civilization. The discovery of new materials or new scientific phenomena, or an improved understanding of the known phenomena requires exploration through the space available for a given
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16

Hraber, Peter T. "Discovering molecular mechanisms of mututalism with computational approaches to endosymbiosis /." Color figures, full content, and supplementary materials are available online, 2001.

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Thesis (Ph. D.)--University of New Mexico, 2001.<br>"July, 2001." Includes bibliographical references (leaves 112-121). Color figures, full content, and supplementary materials are available online via www.santafe.edu/p̃th/dss.
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17

Patel-Murray, Natasha L. (Natasha Leanna). "Understanding neurodegenerative disease-relevant molecular effects of perturbagens using a multi-omics approach." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122721.

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Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2019<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>The complex etiology of neurodegenerative diseases is not fully understood, and the characterization of cellular pathways that are dysfunctional in these diseases is key for therapeutic development. Chemical and genetic perturbagens can probe cellular pathways to shed insight about both disease etiology and potential therapeutic targets. We analyzed the functional effects of chemical perturbagens in neurodegen
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18

Almeida, André Atanasio Maranhão 1981. "Comparação algebrica de genomas : o caso da distancia de reversão." [s.n.], 2007. http://repositorio.unicamp.br/jspui/handle/REPOSIP/276265.

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Orientador: João Meidanis<br>Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Computação<br>Made available in DSpace on 2018-08-08T13:34:53Z (GMT). No. of bitstreams: 1 Almeida_AndreAtanasioMaranhao_M.pdf: 3188069 bytes, checksum: b0743bc208c47e2d263f7d5503c22c07 (MD5) Previous issue date: 2007<br>Resumo: Nas últimas décadas presenciamos grandes avanços na biologia molecular que levaram ao acúmulo de um grande volume de dados acerca de moléculas, tais como DNAs e proteínas, essenciais para a vida e para seu entendimento.O estágio atual é de busca por ferramentas que p
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19

Yang, Darren. "Exploring Biomolecular Interactions Through Single-Molecule Force Spectroscopy and Computational Simulation." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493410.

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Molecular interactions between cellular components such as proteins and nucleic acids govern the fundamental processes of living systems. Technological advancements in the past decade have allowed the characterization of these molecular interactions at the single-molecule level with high temporal and spatial resolution. Simultaneously, progress in computer simulation has enabled theoretical research at the atomistic level, assisting in the interpretation of experimental results. This thesis combines single-molecule force spectroscopy and simulation to explore inter- and intra-molecular inte
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20

Dutta, Priyanka. "Computational Modeling of Allosteric Stimulation of Nipah Virus Host Binding Protein." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6227.

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Nipah belongs to the family of paramyxoviruses that cause numerous fatal diseases in humans and farm animals. There are no FDA approved drugs for Nipah or any of the paramyxoviruses. Designing antiviral therapies that are more resistant to viral mutations require understanding of molecular details underlying infection. This dissertation focuses on obtaining molecular insights into the very first step of infection by Nipah. Such details, in fact, remain unknown for all paramyxoviruses. Infection begins with the allosteric stimulation of Nipah virus host binding protein by host cell receptors. U
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21

Hanson-Smith, Victor 1981. "Error and Uncertainty in Computational Phylogenetics." Thesis, University of Oregon, 2011. http://hdl.handle.net/1794/12151.

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xi, 119 p. : ill. (some col.)<br>The evolutionary history of protein families can be difficult to study because necessary ancestral molecules are often unavailable for direct observation. As an alternative, the field of computational phylogenetics has developed statistical methods to infer the evolutionary relationships among extant molecular sequences and their ancestral sequences. Typically, the methods of computational phylogenetic inference and ancestral sequence reconstruction are combined with other non-computational techniques in a larger analysis pipeline to study the inferred forms an
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22

Ainsley, Jon. "Computational simulations of enzyme dynamics and the modelling of their reaction mechanisms." Thesis, Northumbria University, 2017. http://nrl.northumbria.ac.uk/36286/.

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Proteins and enzymes are large and complex biological molecules, characterized by unique three-dimensional structure are highly flexible and dynamic nature. Thorough understanding of protein and enzyme function requires studying of their conformational flexibility, because important physiological processes, such as ligand binding and catalysis rely on an enzyme’s dynamic nature and their ability to adopt a variety of conformational states. Computational methods are widely applied in studying enzymes and proteins structure and function providing a detailed atomistic-level of resolution data abo
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23

Rho, Mina. "Probabilistic models in computational molecular biology applied to the identification of mobile genetic elements and gene finding." [Bloomington, Ind.] : Indiana 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:3386714.

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Thesis (Ph.D.)--Indiana University, School of Informatics and Computing, 2009.<br>Title from PDF t.p. (viewed on Jul 22, 2010). Source: Dissertation Abstracts International, Volume: 70-12, Section: B, page: 7299. Adviser: Haixu Tang.
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24

Mathuriya, Amrita. "Prediction of secondary structures for large RNA molecules." Thesis, Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28195.

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Thesis (M. S.)--Computing, Georgia Institute of Technology, 2009.<br>Committee Chair: Bader, David; Committee Co-Chair: Heitsch, Christine; Committee Member: Harvey, Stephen; Committee Member: Vuduc, Richard.
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25

Chotikasemsri, Pongsathorn. "Computational Prediction of the Agregated Structure of Denatured Lysozyme." TopSCHOLAR®, 2009. http://digitalcommons.wku.edu/theses/120.

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Mis-folded proteins and their associated aggregates are a contributing factor in some human diseases. In this study we used the protein lysozyme as a model to define aggregation structures under denaturing conditions. Sasahara et al. (2007), Frare et al. (2009, 2006), and Rubin et al. (2008) observed conditions where heat denatured lysozyme formed fibril structures that were observed to be 8-17 nanometers in diameter under the electron microscope. Even though the crystal structure of lysozyme is known, the denatured form of this protein is still unknown. Therefore, we used Rosetta++ protein fo
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26

Usié, Chimenos Anabel. "Development of computational tools to assist in the reconstruction of molecular networks." Doctoral thesis, Universitat de Lleida, 2014. http://hdl.handle.net/10803/129848.

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L'objectiu d'aquesta tesi és desenvolupar i implementar un conjunt d'eines de mineria de dades per ajudar en la reconstrucció de circuits biològics a través de l'anàlisi i la integració de grans conjunts de dades biològiques. Aquests circuits són importants perquè regulen tots els processos que controlen la vida i la salut dels organismes. El treball principal de la tesis es centra en l'anàlisi de les dades bibliòmiques desenvolupant-se dues eines, Biblio-MetReS per la reconstrucció de xarxes de PPIs i la identificació dels processos en què intervenen aquestes xarxes, i CheNER per la identifi
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Ruiz, Carmona Sergio. "Virtual screening for novel mechanisms of action: applications and methodological developments." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/400297.

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The main motivation of this thesis has been to validate, improve and develop new methods with respect to the ones available nowadays in the area of drug discovery, in order to be able to study more challenging targets in the near future that currently are out of our reach. As the productivity of the pharmaceutical industry is decreasing year after year over the last decades, the improvement of such methods would be a step forward. As we are mostly a computational lab, this thesis has focused on different computational approaches such as docking, molecular dynamics or chemoinformatics. O
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28

Österberg, Fredrik. "Exploring Ligand Binding in HIV-1 Protease and K+ Channels Using Computational Methods." Doctoral thesis, Uppsala universitet, Strukturell molekylärbiologi, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6167.

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Understanding protein-ligand interactions is highly important in drug development. In the present work the objective is to comprehend the link between structure and function using molecular modelling. Specifically, this thesis has been focused on implementation of receptor flexibility in molecular docking and studying structure-activity relationships of potassium ion channels and their blockers. In ligand docking simulations protein motion and heterogeneity of structural waters are approximated using an ensemble of protein structures. Four methods of combining multiple target structures within
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29

Paissoni, C. "COMPUTATIONAL TECHNIQUES TO EVALUATE AT ATOMIC LEVEL THE MECHANISM OF MOLECULAR BINDING." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/480031.

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Integrins are an important class of transmembrane receptors that relay signals bidirectionally across the plasma membrane, regulating several cell functions and playing a key role in diverse pathological processes. Specifically, integrin subtype αIIbβ3 is involved in thrombosis and stroke, while subtypes αvβ3 and α5β1 play an important role in angiogenesis and tumor progression. They therefore emerged as attractive pharmacological targets. In the past decades several peptides and peptidomimetics targeting these proteins and based on the integrin recognition motif RGD (Arg-Gly-Asp) have been de
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30

Olivier, Brett Gareth. "Simulation and database software for computational systems biology : PySCes and JWS Online." Thesis, Stellenbosch : Stellenbosch University, 2005. http://hdl.handle.net/10019.1/50449.

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Thesis (PhD)--Stellenbosch University, 2005.<br>ENGLISH ABSTRACT: Since their inception, biology and biochemistry have been spectacularly successful in characterising the living cell and its components. As the volume of information about cellular components continues to increase, we need to ask how we should use this information to understand the functioning of the living cell? Computational systems biology uses an integrative approach that combines theoretical exploration, computer modelling and experimental research to answer this question. Central to this approach is the development o
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31

Stemm, Mina Catherine. "Computational and combinatorial design of protein-based inhibitors of human tyrosyl-DNA phosphodiesterase /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2005. http://wwwlib.umi.com/cr/ucsd/fullcit?p3166399.

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32

Sandal, Massimo Verfasser], Paolo [Akademischer Betreuer] Carloni, and Marc [Akademischer Betreuer] [Spehr. "Finding common structural traits of GPCRs by computational molecular biology approaches / Massimo Sandal ; Paolo Carloni, Marc Spehr." Aachen : Universitätsbibliothek der RWTH Aachen, 2016. http://d-nb.info/1126040908/34.

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Sandal, Massimo [Verfasser], Paolo Akademischer Betreuer] Carloni, and Marc [Akademischer Betreuer] [Spehr. "Finding common structural traits of GPCRs by computational molecular biology approaches / Massimo Sandal ; Paolo Carloni, Marc Spehr." Aachen : Universitätsbibliothek der RWTH Aachen, 2016. http://d-nb.info/1126040908/34.

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34

Baudet, Christian. "Enumeração de traces e identificação de breakpoints = estudo de aspectos da evolução." Universidade Estadual de Campinas. Instituto de Computação, 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/275773.

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Orientador: Zanoni Dias<br>Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Computação<br>Made available in DSpace on 2018-08-17T08:10:32Z (GMT). No. of bitstreams: 1 Baudet_Christian_D.pdf: 3490604 bytes, checksum: 7f0a8868574d06e11524e5a5de9d1fd0 (MD5) Previous issue date: 2010<br>Resumo: O estudo de rearranjo de genomas tem o objetivo de auxiliar o entendimento da evolução. Através da análise dos eventos de mutação como inversões, transposições, fissões, fusões, entre outros, buscamos compreender as suas influências sobre o fenômeno da diferenciação das espécies. Dentro
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35

Mohammadiarani, Hossein. "Simulation Studies of Signaling and Regulatory Proteins." Thesis, University of New Hampshire, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10685640.

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<p> I used molecular dynamics (MD) simulations as a primary tool to study folding and dynamics of signaling and regulatory proteins. Specifically, I have studied two classes of proteins: the first part of my thesis reports studies on peptides and receptors of the insulin family, and the second part reports on studies of regulatory proteins from the G-protein coupled receptor family. The first problem that I investigated was understanding the folding mechanism of the insulin B-chain and its mimetic peptide (S371) which were studied using enhanced sampling simulation methods. I validated our sim
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Bauer, Paul. "Computational modelling of enzyme selectivity." Doctoral thesis, Uppsala universitet, Struktur- och molekylärbiologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-326108.

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Enantioselective reactions are one of the ways to produce pure chiral compounds. Understanding the basis of this selectivity makes it possible to guide enzyme design towards more efficient catalysts. One approach to study enzymes involved in chiral chemistry is through the use of computational models that are able to simulate the chemical reaction taking place. The potato epoxide hydrolase is one enzyme that is known to be both highly enantioselective, while still being robust upon mutation of residues to change substrate scope. The enzyme was used to investigate the epoxide hydrolysis mechani
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Belknap, Ethan M. "Computational Model of the Nucleophilic Acyl Substitution Pathway." Wittenberg University Honors Theses / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=wuhonors1623251026132848.

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Jones, Thomas Carroll Jr. "JigCell Model Connector: Building Large Molecular Network Models from Components." Thesis, Virginia Tech, 2017. http://hdl.handle.net/10919/78277.

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The ever-growing size and complexity of molecular network models makes them difficult to construct and understand. Modifying a model that consists of tens of reactions is no easy task. Attempting the same on a model containing hundreds of reactions can seem nearly impossible. We present the JigCell Model Connector, a software tool that supports large-scale molecular network modeling. Our approach to developing large models is to combine together smaller models, making the result easier to comprehend. At the base, the smaller models (called modules) are defined by small collections of reactions
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Saha, Mandal Arnab. "Computational Analysis of the Evolution of Non-Coding Genomic Sequences." University of Toledo Health Science Campus / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=mco1372349811.

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Marpuri, ReddySalilaja. "Evaluation of Annotation Performances between Automated and Curated Databases of E.COLI Using the Correlation Coefficient." TopSCHOLAR®, 2009. http://digitalcommons.wku.edu/theses/94.

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This project compared the performance of the correlation coefficient to show similarities in annotations between a predictive automated bacterial annotation database and the curated EcoCyc database. EcoCyc is a conservative multidimensional annotation system that is exclusively based on experimentally validated findings by over 15,000 publications. The automated annotation system, used in the comparison was BASys. It is often used as a first pass annotation tool that tries to add as many annotations as possible by drawing upon over 30 information sources. Gene ontology served as one basis of c
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Chakraborty, Promita. "A Computational Framework for Interacting with Physical Molecular Models of the Polypeptide Chain." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/47932.

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Although nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees-of-freedom in the peptide backbone. The coarse-grained backbone model cons
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42

Willems, Nathalie. "Molecular dynamics simulations of lipase-surface interactions." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:7765c334-7c02-4190-a4b2-99ad315cfe52.

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Lipases are enzymes that play fundamental roles in fat digestion and metabolism, and function at the interface formed between hydrophobic molecules and the surrounding aqueous environment. These interfacial interactions are thought to induce conformational changes in a "lid" region of the lipase, leading to a dramatic increase in activity. This thesis aims to provide insight into the interactions that govern lipase association with interfaces of di erent structural characteristics, and the possible conformational changes that arise as a function of these interactions. A multi-scale molecular s
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Chen, Sih-Yu. "Computational studies of biomolecules." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/11064.

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In modern drug discovery, lead discovery is a term used to describe the overall process from hit discovery to lead optimisation, with the goal being to identify drug candidates. This can be greatly facilitated by the use of computer-aided (or in silico) techniques, which can reduce experimentation costs along the drug discovery pipeline. The range of relevant techniques include: molecular modelling to obtain structural information, molecular dynamics (which will be covered in Chapter 2), activity or property prediction by means of quantitative structure activity/property models (QSAR/QSPR), wh
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44

Carlsson, Jens. "Challenges in Computational Biochemistry: Solvation and Ligand Binding." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8738.

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<p>Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding.</p><p>The thermodynamic integration technique is used to calculate p<i>K</i><sub>a</sub> values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated p<i>K</i><sub>a</
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45

Hirst-Dunton, Thomas Alexander. "Using molecular simulations to parameterize discrete models of protein movement in the membrane." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:893568e9-696f-47e7-8495-59ecfb810459.

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The work presented in this thesis centres on the development of a work-flow in which coarse-grained molecular dynamics (MD) simulations of a planar phospholipid bilayer, containing membrane proteins, is used to parameterize a larger-scale simplified bilayer model. Using this work-flow, repeat simulations and simulations of larger systems are possible, better enabling the calculation of bulk statistics for the system. The larger-scale simulations can be run on commercial hardware, once the initial parameterization has been performed. In the simplified representation, each protein was initially
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Gossett, John Jared. "Analysis of macromolecular structure through experiment and computation." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/51925.

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This thesis covers a wide variety of projects within the domain of computational structural biology. Structural biology is concerned with the molecular structure of proteins and nucleic acids, and the relationship between structure and biological function. We used molecular modeling and simulation, a purely computational approach, to study DNA-linked molecular nanowires. We developed a computational tool that allows potential designs to be screened for viability, and then we used molecular dynamics (MD) simulations to test their stability. As an example of using molecular modeling to create ex
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Kucharavy, Andrei. "Molecular mechanisms of aneuploidy-mediated stress-resistance." Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066734.pdf.

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L’aneuploïdie a été historiquement associé à des phénotypes nuisibles, notamment le cancer et le syndrome de Down. Cependant, des résultats expérimentaux récents suggèrent que l’aneuploïdie permettrait l'adaptation à des stresseurs variés, notamment résistance aux médicaments, en rendant la compréhension critique au domaine biomédical. Cependant, les mécanismes moléculaires permettant cette adaptation restaient à élucider. Une telle élucidation selon plusieurs axes a été justement l'objet de ce travail. Premièrement, nous avons développé un modèle mathématique représentant l'adaptation aux env
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Moix, Jeremy Michael. "Molecular Dynamics and Stochastic Simulations of Surface Diffusion." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/14580.

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Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this void. To this end, parallel molecular dynamics simulations of self-diffusion on metal surfaces have been developed and employed to address microscopic details of the system. However these simulations are not without their limitations and prove to be computationally impractical for a variety of chemi
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Andér, Martin. "Computational Analysis of Molecular Recognition Involving the Ribosome and a Voltage Gated K+ Channel." Doctoral thesis, Uppsala universitet, Institutionen för cell- och molekylärbiologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-101413.

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Over the last few decades, computer simulation techniques have been established as an essential tool for understanding biochemical processes. This thesis deals mainly with the application of free energy calculations to ribosomal complexes and a cardiac ion channel. The linear interaction energy (LIE) method is used to explore the energetic properties of the essential process of codon–anticodon recognition on the ribosome. The calculations show the structural and energetic consequences and effects of first, second, and third position mismatches in the ribosomal decoding center. Recognition of s
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Lang, Tiange. "Evolution of transmembrane and gel-forming mucins studied with bioinformatic methods /." Göteborg : The Sahlgrenska Academy at Göteborg University, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, 2007. http://hdl.handle.net/2077/7502.

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