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Dissertations / Theses on the topic 'Computational protein design'

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Published: 4 June 2021

Last updated: 25 July 2025

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1

Traore, Seydou. "Computational approaches toward protein design." Thesis, Toulouse, INSA, 2014. http://www.theses.fr/2014ISAT0033/document.

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Le Design computationnel de protéines, en anglais « Computational Protein Design » (CPD), est un champ derecherche récent qui vise à fournir des outils de prédiction pour compléter l'ingénierie des protéines. En effet,outre la compréhension théorique des propriétés physico-chimiques fondamentales et fonctionnelles desprotéines, l’ingénierie des protéines a d’importantes applications dans un large éventail de domaines, y comprisdans la biomédecine, la biotechnologie, la nanobiotechnologie et la conception de composés respectueux del’environnement. Le CPD cherche ainsi à accélérer le design de p

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2

Wood, Christopher Robin Wells. "Computational design of parameterisable protein folds." Thesis, University of Bristol, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.715832.

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3

Hong, Eun-Jong 1975. "Exact rotamer optimization for computational protein design." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/44421.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.<br>Includes bibliographical references (leaves 235-244).<br>The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization problem. Dead-end elimination (DEE) methods combined with systematic A* search (DEE/A*) have proven useful, but may not be strong enough as we attempt to solve protein design problem

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4

Biddle, Jason Charles. "Methods and applications in computational protein design." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/61792.

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Thesis (S.M.)--Massachusetts Institute of Technology, Computation for Design and Optimization Program, 2010.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Cataloged from student-submitted PDF version of thesis.<br>Includes bibliographical references (p. 107-111).<br>In this thesis, we summarize our work on applications and methods for computational protein design. First, we apply computational protein design to address the problem of degradation in stored proteins. Specifically, we target

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5

Fuller, Jonathan Christopher. "Computational approaches for drug design at the protein-protein interface." Thesis, University of Leeds, 2010. http://etheses.whiterose.ac.uk/1699/.

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The ability to design drugs that disrupt formation of protein-protein interfaces is of particular interest to the pharmaceutical industry due to its promise for opening an entire new range of drug targets, many of which have already been well characterised in terms of their disease causing effect on the human body. Furthermore these interactions can be involved in many processes unique and essential to bacteria and viruses. We show that pockets on protein-protein interface are smaller but more numerous than those of marketed drugs using a pocket fnding algorithm (Q-SiteFinder). We investigate

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6

Davey, James A. "Multistate Computational Protein Design: Theories, Methods, and Applications." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35541.

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Traditional computational protein design (CPD) calculations model sequence perturbations and evaluate their stabilities using a single fixed protein backbone template in an approach referred to as single‐state design (SSD). However, certain design objectives require the explicit consideration of multiple conformational states. Cases where a multistate framework may be advantageous over the single‐state approach include the computer aided discovery of new enzyme substrates, the prediction of protein stabilities, and the design of protein dynamics. These design objectives can be tackled using mu

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7

MARCHETTI, FILIPPO. "COMPUTATIONAL STUDIES OF PROTEIN-PROTEIN AND PROTEIN-ANTIBODY INTERACTIONS: IMPLICATION FOR MOLECULAR DESIGN." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/825462.

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High performance computing has opened the possibility to investigate complex systems by simulating their dynamics and study of equilibrium and non-equilibrium settings in realistic settings. Molecular Dynamics (MD) simulations have emerged as one of the privileged methods to disentangle the intricacies of biochemical systems but, despite the validity of Moore’s Law, the timescale of the events that can be simulated has an upper limit of the millisecond with tailor-made computers which is not enough to study some biologically relevant phenomena. Starting from these considerations, in this thes

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8

Grigoryan, Gevorg Ph D. Massachusetts Institute of Technology. "Computational approaches for the design and prediction of protein-protein interactions." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/38997.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2007.<br>Includes bibliographical references (leaves 167-187).<br>There is a large class of applications in computational structural biology for which atomic-level representation is crucial for understanding the underlying biological phenomena, yet explicit atomic-level modeling is computationally prohibitive. Computational protein design, homology modeling, protein interaction prediction, docking and structure recognition are among these applications. Models that are commonly applied to these problems combine atomic-lev

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9

Park, Daniel J. (Daniel John) 1979. "Computational tools for including specificity in protein design." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/87286.

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10

Sisu, Cristina Smaranda Domnica. "Computational studies on protein similarity, specificity and design." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609407.

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11

Lucato, Arianna <1991&gt. "Computational design of novel protein-drug delivery systems." Master's Degree Thesis, Università Ca' Foscari Venezia, 2019. http://hdl.handle.net/10579/16136.

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Cancer is one of the leading causes of death throughout the world and the number of cases per year is reported to rise to 23.6 million by 2030. Amongst the different types of treatments available, chemotherapy represent the most common one. Despite its proven capability of tumour shrinkage and prevention from coming back after surgery, several factors limit its potential. These include poor bioavailability and biodistribution of the majority of the chemotherapeutic agents commonly used, the high dose required, their numerous adverse side effects, the development of drug resistance and non-spec

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12

Opuu, Vaitea. "Computational design of proteins and enzymes." Thesis, Institut polytechnique de Paris, 2020. http://www.theses.fr/2020IPPAX081.

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Nous proposons un ensemble de méthodes pour la conception de systèmes moléculaires. Notre stratégie consiste à utiliser comme modèle des machines naturellement optimisées, les protéines. Les protéines peuvent être des briques structurales, des transporteurs d'informations ou des catalyseurs chimiques. Nous utilisons ici des approches computationnelles, complémentaires aux voies expérimentales, pour concevoir de tels systèmes.Nous avons d'abord entièrement redessiné un domaine PDZ impliqué dans des voies métaboliques. Nous utilisons une approche physics-based basée sur la mécanique moléculaire,

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13

Jiang, Lin. "Novel catalysts by computational enzyme design /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9248.

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14

Humphris, Elisabeth Lyn. "Computational protein design with multiple functional and structural constraints." Diss., Search in ProQuest Dissertations & Theses. UC Only, 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:3390110.

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15

Henne, Randal Marlow. "Computational studies of G-protein coupled receptors /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/8048.

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16

Dantas, Gautam. "In silico protein evolution by intelligent design : creating new and improved protein structures /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9236.

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17

Chen, Tsan-Chou Scott. "Design of protein-protein interaction specificity using computational methods and experimental library screening." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/70386.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2012.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>Computational design of protein-protein interaction specificity is a powerful tool to examine and expand our understanding about how protein sequence determines interaction specificity. It also has many applications in basic bioscience and biotechnology. One of the major challenges for design is that current scoring functions relying on general physical principles do not always make reliable predictions about interaction specificity

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18

Maffucci, I. "OPTIMIZATION AND APPLICATION OF COMPUTATIONAL METHODS FOR THE DESIGN OF PROTEIN-PROTEIN INTERACTIONS MODULATORS." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/344181.

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In the wide field of PPIs, this PhD project has been focused on the optimization and application of computational methods for the design of PPIs modulators, with a particular interest toward peptide modulators targeting PPIs involving helical motifs. In this contest, the first part of the project has been aimed to define the rationales behind the helical secondary structure stabilization and the helical screw sense selectivity exerted by chiral Cα-tetrasubstituted amino acids (cCTAAs) through REMD simulations and QTAIM analyses, and the mechanisms responsible of the helical screw sense invers

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19

Joughin, Brian Alan. "Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/38630.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2007.<br>Includes bibliographical references (p. 107-130).<br>This thesis presents a number of novel computational methods for the analysis and design of protein-protein complexes, and their application to the study of the interactions of phosphopeptides with phosphopeptide-binding domain interactions. A novel protein-protein interaction type, the action-at-a-distance interaction, is described in the complex of the TEM1 P-lactamase with the 3-lactamase inhibitor protein (BLIP). New action-at-a-distance interactions were

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20

Leaver-Fay, Andrew Snoeyink Jack. "Capturing atomic interactions with a graphical framework in computational protein design." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2006. http://dc.lib.unc.edu/u?/etd,613.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2006.<br>Title from electronic title page (viewed Oct. 10, 2007). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Computer Science." Discipline: Computer Science; Department/School: Computer Science.

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21

Doudou, Slimane. "Computational modelling of protein-ligand binding : steps towards better drug design." Thesis, University of Manchester, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.498949.

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22

Bastianelli, Giacomo. "Computational design of protein-based serine proteases inhibitors : tools and applications." Paris 7, 2009. http://www.theses.fr/2009PA077175.

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PfSUBl et PfSUB2 sont deux régulateurs de l'étape érythrocytaires du parasite et représentent de nouvelles cibles thérapeutiques intéressantes pour le développement de nouvelles familles de composés contre le paludisme. La limite majeure pour un tel développement rationnel de molécule sur les PFSUBs reste l'absence de structures expérimentales et des difficultés à exprimer l'enzyme recombinante active en grande quantité. L'utilisation d'un criblage à haut débit n'est donc pas envisageable à ce jour. Afin de contourner ces problèmes, nous avons mis en place une stratégie de recherche rationnell

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23

Durani, Venuka. "The Cycle of Protein Engineering: Bioinformatics Design of Two Dimeric Proteins and Computational Design of a Small Globular Domain." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1338311626.

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24

Legault, Sandrine. "Investigating Different Rational Design Approaches to Increase Brightness in Red Fluorescent Proteins." Thesis, Université d'Ottawa / University of Ottawa, 2021. http://hdl.handle.net/10393/42740.

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Red fluorescent proteins (RFPs) are used extensively in biological research because their longer emission wavelengths are less phototoxic and allow deeper imaging of animal tissue. However, far-red RFPs generally display low brightness, emphasizing the need to develop brighter variants. Here, we investigate three approaches to rigidify the RFP chromophore to increase the quantum yield, and thereby brightness. We first used computational protein design on a maturation-efficient mRojo-VHSV variant previously engineered in our lab to introduce a Superdecker motif, a parallel pi-stack comprising a

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25

Vankayala, Sai Lakshmana Kumar. "Computational Approaches for Structure Based Drug Design and Protein Structure-Function Prediction." Scholar Commons, 2013. http://scholarcommons.usf.edu/etd/4601.

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This dissertation thesis consists of a series of chapters that are interwoven by solving interesting biological problems, employing various computational methodologies. These techniques provide meaningful physical insights to promote the scientific fields of interest. Focus of chapter 1 concerns, the importance of computational tools like docking studies in advancing structure based drug design processes. This chapter also addresses the prime concerns like scoring functions, sampling algorithms and flexible docking studies that hamper the docking successes. Information about the different kin

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26

Toschi, Francesca. "The computational investigation of protein/ligand complexes : implications for rational drug design." Thesis, University of Southampton, 2004. https://eprints.soton.ac.uk/378844/.

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27

St-Jacques, Antony D. "Engineering of Multi-Substrate Enzyme Specificity and Conformational Equilibrium Using Multistate Computational Protein Design." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/38590.

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The creation of enzymes displaying desired substrate specificity is an important objective of enzyme engineering. To help achieve this goal, computational protein design (CPD) can be used to identify sequences that can fulfill interactions required to productively bind a desired substrate. Standard CPD protocols find optimal sequences in the context of a single state, for example an enzyme structure with a single substrate bound at its active site. However, many enzymes catalyze reactions requiring them to bind multiple substrates during successive steps of the catalytic cycle. The design of m

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28

Gagnon, Olivier. "Development and Validation of a Structure-Based Computational Method for the Prediction of Protein Specificity Profiles." Thesis, Université d'Ottawa / University of Ottawa, 2019. http://hdl.handle.net/10393/39643.

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Post-translational modification (PTM) of proteins by enzymes such as methyltransferases, kinases and deacetylases play a crucial role in the regulation of many metabolic pathways. Determining the substrate scope of these enzymes is essential when studying their biological role. However, the combinatorial nature of possible protein substrate sequences makes experimental screening assays intractable. To predict new substrates for proteins, various computational approaches have been developed. Our method relies on crystallographic data and a novel multistate computational protein design algorithm

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29

Shah, Premal S. Rees Douglas C. "Advances in force field development and sequence optimization methods for computational protein design /." Diss., Pasadena, Calif. : California Institute of Technology, 2005. http://resolver.caltech.edu/CaltechETD:etd-04042005-142719.

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30

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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31

Mignon, David. "Computational protein design : un outil pour l'ingénierie des protéines et la biologie synthétique." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX089/document.

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Le « Computational protein design » ou CPD est la recherche des séquences d’acides aminés compatibles avec une structure protéique ciblée. L’objectif est de concevoir une fonction nouvelle et/ou d’ajouter un nouveau comportement. Le CPD est en développement dans de notre laboratoire depuis plusieurs années, avec le logiciel Proteus qui a plusieurs succès à son actif.Notre approche utilise un modèle énergétique basé sur la physique et s’appuie sur la différence d’énergie entre l’état plié et l’état déplié de la protéine. Au cours de cette thèse, nous avons enrichi Proteus sur plusieurs points,

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32

Hom, Geoffrey Deshaies Raymond Joseph. "Advances in computational protein design : development of more efficient search algorithms and their application to the full-sequence design of larger proteins /." Diss., Pasadena, Calif. : California Institute of Technology, 2005. http://resolver.caltech.edu/CaltechETD:etd-05302005-223153.

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33

GULOTTA, Maria Rita. "Computational methodologies applied to Protein-Protein Interactions for molecular insights in Medicinal Chemistry." Doctoral thesis, Università degli Studi di Palermo, 2021. http://hdl.handle.net/10447/479127.

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In living systems, proteins usually team up into “molecular machinery” implementing several protein-to-protein physical contacts – or protein-protein interactions (PPIs) – to exert biological effects at both cellular and systems levels. Deregulations of protein-protein contacts have been associated with a huge number of diseases in a wide range of medical areas, such as oncology, cancer immunotherapy, infectious diseases, neurological disorders, heart failure, inflammation and oxidative stress. PPIs are very complex and usually characterised by specific shape, size and complementarity. The pr

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34

Feldmeier, Kaspar Konrad [Verfasser], and Birte [Akademischer Betreuer] Höcker. "Form and Function : Two computational protein design studies / Kaspar Konrad Feldmeier ; Betreuer: Birte Höcker." Tübingen : Universitätsbibliothek Tübingen, 2016. http://d-nb.info/1164169718/34.

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35

Ross, Gregory A. "Improving rapid affinity calculations for drug-protein interactions." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:62ccfb5e-10f1-40ec-9a2b-936277944d87.

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The rationalisation of drug potency using three-dimensional structures of protein-ligand complexes is a central paradigm in medicinal research. For over two decades, a major goal has been to find the rules that accurately relate the structure of any protein-ligand complex to its affinity. Addressing this problem is of great concern to the pharmaceutical industry, which uses virtual screens to computationally assay up to many millions of compounds against a protein target. A fast and trustworthy affinity estimator could potentially streamline the drug discovery process, reducing reliance on exp

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36

Denarie, Laurent. "Robotics-inspired methods to enhance protein design." Phd thesis, Toulouse, INPT, 2017. http://oatao.univ-toulouse.fr/18677/1/Denarie.pdf.

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The ability to design proteins with specific properties would yield great progress in pharmacology and bio-technologies. Methods to design proteins have been developed since a few decades and some relevant achievements have been made including de novo protein design. Yet, current approaches suffer some serious limitations. By not taking protein’s backbone motions into account, they fail at capturing some of the properties of the candidate design and cannot guarantee that the solution will in fact be stable for the goal conformation. Besides, although multi-states design methods have been propo

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37

Capelli, R. "COMPUTATIONAL MODELING OF PROTEINS: FROM STATISTICAL MECHANICS TO IMMUNOLOGY." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/527950.

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One of the biggest revolutions occurred during the second half of the 20th century in physics was the introduction of computers in research. In particular, the use of fast computing machines opened the possibility to study complex systems by simulating their dynamics, without the need to pursue analytical solutions, otherwise impossible to tackle. The consequences of this breakthrough were huge both in the study of equilibrium and non-equilibrium many-body problems, with the strong limitation given by the number of atoms involved in the calculation. The first technique used in biology-related

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38

Druart, Karen. "Défis algorithmiques pour les simulations biomoléculaires et la conception de protéines." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLX080/document.

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Le dessin computationnel de protéine, ou CPD, est une technique qui permet de modifier les protéines pour leur conférer de nouvelles propriétés, en exploitant leurs structures 3D et une modélisation moléculaire. Pour rendre la méthode de plus en plus prédictive, les modèles employés doivent constamment progresser. Dans cette thèse, nous avons abordé le problème de la représentation explicite de la flexibilité du squelette protéique. Nous avons développé une méthode de dessin "multi-états", qui se base sur une bibliothèque discrète de conformations du squelette, établie à l'avance. Dans un cont

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39

Badieyan, Somayesadat. "Molecular Design and Mechanistic Characterization of Glycoside Hydrolases using Computational and Experimental Techniques." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/77989.

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Cellulase activity is due to the activity of multiple enzymes, including endoglucanases, cellobiohydrolases and glucosidases that work synergistically to solubilize crystalline cellulose efficiently. The dependence of hydrolysis reaction rate on temperature predicts that large increases in performance and decreased enzyme cost would be achieved if the enzymatic degradation could be operated at elevated temperatures. However there is always a tradeoff between the activity and stability of enzymes. So obtaining cellulases with high thermostability and simultaneously enhanced activity is a great

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40

Correia, Bruno Emanuel Ferreira de Sousa. "Computational design with flexible backbone sampling for protein remodeling and scaffolding of complex binding sites." Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, 2010. http://hdl.handle.net/10362/5791.

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Dissertation presented to obtain the Doutoramento (Ph.D.) degree in Biochemistry at the Instituto de Tecnologia Qu mica e Biol ogica da Universidade Nova de Lisboa<br>Computational protein design has achieved several milestones, including the design of a new protein fold, the design of enzymes for reactions that lack natural catalysts, and the re-engineering of protein-protein and protein-DNA binding speci city. These achievements have spurred demand to apply protein design methods to a wider array of research problems. However, the existing computational methods have largely relied on

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Fang, Lei. "COMPUTATIONAL MODELING, DESIGN, AND CHARACTERIZATION OF COCAINE-METABOLIZING ENZYMES FOR ANTI-COCAINE MEDICATION." UKnowledge, 2013. http://uknowledge.uky.edu/pharmacy_etds/39.

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Cocaine is a widely abused and addictive drug, resulting in serious medical and social problems in modern society. Currently, there is no FDA-approved medication specific for cocaine abuse treatment. The disastrous medical and social consequences of cocaine abuse have made the development of an anti-cocaine medication a high priority. However, despite decades of efforts, traditional pharmacodynamic approach has failed to yield a truly useful small-molecule drug due to the difficulties inherent in blocking a blocker like cocaine without affecting the normal functions of the transporters or rece

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42

Li, Weiyi. "Protein Engineering Hydrophobic Core Residues of Computationally Designed Protein G and Single-Chain Rop: Investigating the Relationship between Protein Primary structure and Protein Stability through High-Throughput Approaches." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1398956266.

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43

Domin, Gesine, Sven Findeiß, Manja Wachsmuth, Sebastian Will, Peter F. Stadler, and Mario Mörl. "Applicability of a computational design approach for synthetic riboswitches." Universitätsbibliothek Leipzig, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-218007.

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Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand dependent transcription termination in Escherichia coli. Here, we test t

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44

Domin, Gesine, Sven Findeiß, Manja Wachsmuth, Sebastian Will, Peter F. Stadler, and Mario Mörl. "Applicability of a computational design approach for synthetic riboswitches." Oxford University Press, 2016. https://ul.qucosa.de/id/qucosa%3A15259.

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Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand dependent transcription termination in Escherichia coli. Here, we test t

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45

Mahasenan, Kiran V. "Discovery of novel small molecule enzyme inhibitors and receptor modulators through structure-based computational design." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1332367560.

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46

Lanouette, Sylvain. "Characterization of the Protein Lysine Methyltransferase SMYD2." Thesis, Université d'Ottawa / University of Ottawa, 2015. http://hdl.handle.net/10393/32467.

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Our understanding of protein lysine methyltransferases and their substrates remains limited despite their importance as regulators of the proteome. The SMYD (SET and MYND domain) methyltransferase family plays pivotal roles in various cellular processes, including transcriptional regulation and embryonic development. Among them, SMYD2 is associated with oesophageal squamous cell carcinoma, bladder cancer and leukemia as well as with embryonic development. Initially identified as a histone methyltransferase, SMYD2 was later reported to methylate p53, the retinoblastoma protein pRb and the estro

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47

Altman, Michael Darren. "Computational ligand design and analysis in protein complexes using inverse methods, combinatorial search, and accurate solvation modeling." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/36258.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006.<br>Vita.<br>Includes bibliographical references (p. 207-230).<br>This thesis presents the development and application of several computational techniques to aid in the design and analysis of small molecules and peptides that bind to protein targets. First, an inverse small-molecule design algorithm is presented that can explore the space of ligands compatible with binding to a target protein using fast combinatorial search methods. The inverse design method was applied to design inhibitors of HIV-1 protease that

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48

González-Alemán, Roy. "Computational fragment-based design of chemically modified oligonucleotides for selective protein inhibition : BACE1 as a case study." Electronic Thesis or Diss., université Paris-Saclay, 2023. http://www.theses.fr/2023UPASL149.

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La conception de médicaments à base de fragments (FBDD) est devenue une approche de plus en plus populaire dans la conception de ligand, avec de nombreuses réussites dans le processus de découverte de médicaments. Malgré certains défis liés à l'accessibilité synthétique et aux stratégies de conception de ligand, le FBDD reste une méthode prometteuse pour aborder l'espace chimique, la complexité moléculaire, la probabilité de liaison et l'efficacité des ligands. Les thérapies à ARN se développent rapidement, subissant une résurgence en raison des nombreux avantages de ces molécules par rapport

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Radoux, Christopher John. "The automatic detection of small molecule binding hotspots on proteins : applying hotspots to structure-based drug design." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/275133.

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Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods typically assess the pocket as a whole, doing little to suggest which regions and interactions are the most important for binding. This thesis introduces Fragment Hotspot Maps, a grid-based method that samples atomic propensities derived from interactions in the Cambridge Structural Database (CSD) with simple molecular probes. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores, offering more precision over other binding site prediction m

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Almlöf, Martin. "Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7421.

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<p>The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.</p><p>For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these

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