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Dissertations / Theses on the topic 'Virtual screening'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Grecu, T. "Virtual cocrystal screening." Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/5929/.

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2

Capuccini, Marco. "Structure-Based Virtual Screening in Spark." Thesis, Uppsala universitet, Institutionen för farmaceutisk biovetenskap, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-257028.

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3

Corbeil, Christopher. "New virtual screening tools for molecular discovery." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40786.

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In the field of molecular discovery, virtually screening large libraries of compounds proved to be often more cost-efficient than the traditional experimental approaches. In fact, it has now become common practice thanks to the virtual screening tools available to chemists in the pharmaceutical industry, specifically docking. Most docking programs do not account for the dynamics associated with protein-ligand binding whether it is protein flexibility or the inclusion of displaceable water molecules. FITTED1.0 was developed to include these specific two features and has been validated on a test

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4

Müller, Christoph H. P. "Similarity-based virtual screening using inference networks." Thesis, University of Sheffield, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531182.

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5

Koutsoukas, Alexios. "Virtual screening and bioactivities of small molecules." Thesis, University of Cambridge, 2014. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708215.

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6

Shave, Steven R. "Development of high performance structure and ligand based virtual screening techniques." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4333.

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Virtual Sreening (VS) is an in silico technique for drug discovery. An overview of VS methods is given and is seen to be approachable from two sides: structure based and ligand based. Structure based virtual screening uses explicit knowledge of the target receptor to suggest candidate receptor-ligand complexes. Ligand based virtual screening can infer required characteristics of binders from known ligands. A consideration for all virtual screening techniques is the amount of computing time required to arrive at a solution. For this reason, techniques of high performance computing have been app

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7

Schellhammer, Ingo. "Structure based molecule indexing for sublinear virtual screening." Berlin Logos-Verl, 2005. http://deposit.ddb.de/cgi-bin/dokserv?id=2820891&prov=M&dok_var=1&dok_ext=htm.

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8

Arif, Shereena M. "Fragment weighting schemes for similarity-based virtual screening." Thesis, University of Sheffield, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540932.

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9

Martin, Richard Luis. "Wavelet approximation of GRID fields for virtual screening." Thesis, University of Sheffield, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531509.

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10

Hert, JeÌroÌ‚me. "Two-dimensional, similarity-based methods for virtual screening." Thesis, University of Sheffield, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.425602.

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11

Psaroudakis, G. "Virtual screening in drug design and model evaluation." Thesis, University of Essex, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.422234.

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12

García, Hernández Carlos Jesús. "Structural Pattern Recognition for Chemical-Compound Virtual Screening." Doctoral thesis, Universitat Rovira i Virgili, 2021. http://hdl.handle.net/10803/673441.

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Les molècules es configuren de manera natural com a xarxes, de manera que són ideals per estudiar utilitzant les seves representacions gràfiques, on els nodes representen àtoms i les vores representen els enllaços químics. Una alternativa per a aquesta representació directa és el gràfic reduït ampliat, que resumeix les estructures químiques mitjançant descripcions de nodes de tipus farmacòfor per codificar les propietats moleculars rellevants. Un cop tenim una manera adequada de representar les molècules com a gràfics, hem de triar l’eina adequada per comparar-les i analitzar-les. La distància

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13

Iglesias, Fernández Jelisa Maria. "Enrichment of virtual screening results using induced-fit techniques." Doctoral thesis, Universitat Politècnica de Catalunya, 2020. http://hdl.handle.net/10803/668826.

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This thesis explains the design, development, test on the benchmarking dataset DUD-e and the application to an industrial virtual screening project of the PELE VS platform. The most common and quick tools used on virtual screening campaigns do not take into account the induced-fit effect, although there are some methodologies capable of reproducing this effect they are either time consuming or very limited on which transformations the protein may undergo. In this thesis with the development of the PELE VS platform we aim at using the simulation software PELE (Protein Energy Landscape Explorat

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14

Fenu, Luca Antonio. "The Development of Novel Scoring Methods for Virtual Screening." Thesis, University of Southampton, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485039.

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Protein ligand docking is a valuable technique in the field of Structure Based Drug Design. One of its applications is to select one orfew candidates from a set of thousands or million compounds, often mmm as Virntal Screening. The choice of the correct scoring function is of paramount importance, and currently available scoring function are most often implemented to optimise reproduction of monn binding modes, or experimental free energies. The vast amount of information contained in the fact that most ligand do not, indeed bind to a given protein is discarded, building a considerable bias in

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15

Schlosser, Jochen [Verfasser]. "Structure-Based Virtual Screening Using Index Technology / Jochen Schlosser." Aachen : Shaker, 2011. http://d-nb.info/1080764321/34.

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16

Weaver, Shane George Thomas. "Stucture and accessibility based screening of virtual combinatorial libraries." Thesis, University of Leeds, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.417726.

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17

Mazalan, Lucyantie. "Evaluation of similarity measures for ligand-based virtual screening." Thesis, University of Sheffield, 2017. http://etheses.whiterose.ac.uk/21422/.

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18

Lewis, Stephanie N. "Refinement of the Docking Component of Virtual Screening for PPAR." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/23675.

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Exploration of peroxisome proliferator-activated receptor-gamma (PPAR") as a drug target holds applications for treating a wide variety of chronic inflammation-related diseases. Type 2 diabetes (T2D), which is a metabolic disease influenced by chronic inflammation, is quickly reaching epidemic proportions. Although some treatments are available to control T2D, more efficacious compounds with fewer side effects are in great demand. Drugs targeting PPAR" typically are compounds that function as agonists toward this receptor, which means they bind to and activate the protein. Identifying compound

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19

Langham, James J. "Discovering drug candidates in virtual chemical libraries : a novel graph-based method for virtual screening /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2006. http://uclibs.org/PID/11984.

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20

Rachman, Moira. "Fragment-to-Lead Optimization with Automated and Iterative Virtual Screening." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/671756.

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Fragment-based drug design is an established strategy of finding new drugs. Instead of doing mass screening of chemical libraries containing compounds that are already lead-like, starting from a small fragment can be be a more efficient strategy, because fragment space can actually represent a much larger chemical space than an equally sized library of lead-like compounds. This strategy has led to the discovery of binders for targets where high-throughput screening has previously failed. However, because fragments are small they bind with low affinity, and must be optimized into high affinity

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21

Tatum, Natalie Joan. "Discovery by virtual screening of ethionamide boosters for tuberculosis treatment." Thesis, Durham University, 2015. http://etheses.dur.ac.uk/11315/.

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Tuberculosis remains the world’s deadliest communicable bacterial disease with an unacceptably high death rate. In 2013 an estimated 1.5 million people died as a direct result of TB, and nine million new cases were reported. Multi-drug resistant (MDR) and extensively drug-resistant (XDR) tuberculosis cases are on the rise and without novel approaches to combat their spread, tuberculosis will continue to claim the lives of millions worldwide. One such novel approach is to rejuvenate the use of the second-line antibiotic ethionamide. Ethionamide is a structural analogue of the first-line pro-dru

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22

Bologna, Fabio <1992&gt. "Development of reverse docking protocols for virtual screening in nanomedicine." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2021. http://amsdottorato.unibo.it/9932/1/bologna_fabio_tesi.pdf.

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One of the first computational chemistry tools that have been used in pharmaceutical research is molecular docking, which infers the interaction between two molecules, usually a small active compound and a receptor, on the basis of their 3D structures. During my three years of PhD studies I worked mainly on re-purposing molecular docking tools to investigate the interactions between a single molecule of interest and a collection of proteins of pharmacological interest. Since this process is essentially the inverse of what is usually done in pharmaceutical research, the technique is called reve

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23

Chirdon, Patrick Edward. "Creation of a Virtual Compound Library for Potential Signal Transduction Modifiers and Virtual Screening Algorithm Pipelines." Ohio University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1607006364917876.

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24

Mavridis, Lazaros. "High throughput virtual drug screening using spherical harmonic molecular surface representations." Thesis, Available from the University of Aberdeen Library and Historic Collections Digital Resources, 2009. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?application=DIGITOOL-3&owner=resourcediscovery&custom_att_2=simple_viewer&pid=25936.

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25

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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26

Marko, Adam Christian. "Structure prediction and virtual screening: Application to G protein-coupled receptors." 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:1469757.

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27

Jacobsson, Micael. "Structure-Based Virtual Screening : New Methods and Applications in Infectious Diseases." Doctoral thesis, Uppsala universitet, Avdelningen för organisk farmaceutisk kemi, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9302.

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A drug discovery project typically starts with a pharmacological hypothesis: that the modulation of a specific molecular biological mechanism would be beneficial in the treatment of the targeted disease. In a small-molecule project, the next step is to identify hits, i.e. molecules that can effect this modulation. These hits are subsequently expanded into hit series, which are optimised with respect to pharmacodynamic and pharmacokinetic properties, through medicinal chemistry. Finally, a drug candidate is clinically developed into a new drug. This thesis concerns the use of structure-based vi

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28

Wood, David. "The use of kernel-based machine learning algorithms in virtual screening." Thesis, University of Sheffield, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.489104.

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The high-throughput technologies of combinatorial chemistry and high-throughput screening have caused an explosion in the amount of data that pharmaceutical companies have available to them in the early stages of drug discovery. These large datasets are frequently analysed with machine learning tools and techniques. In this work, kernel-based machine learning algorithms are assessed and developed for virtual screening purposes using a wide range of molecular representations, and recommendations for improving the accuracy or the activity models are made.

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29

Chen, R. K. H. "Message-oriented light-weight grid : an application to virtual screening procedures." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597536.

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As the quality of computational scientific applications improved over the years, it has made computational modelling a worthy partner of experimental science. However, the power of the supercomputers currently available are no longer sufficient for satisfying the requirements from application scientists. The increasing power of PCs and workstations offers an alternative approach to “inexpensive” high-performance computing. Computational Grids are emerging as a new paradigm for aggregation of heterogeneous and distributed resources for large-scale computing and data intensive problems. One of t

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30

Svensson, Fredrik. "Computational Methods in Medicinal Chemistry : Mechanistic Investigations and Virtual Screening Development." Doctoral thesis, Uppsala universitet, Avdelningen för organisk farmaceutisk kemi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-259443.

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Computational methods have become an integral part of drug development and can help bring new and better drugs to the market faster. The process of predicting the biological activity of large compound collections is known as virtual screening, and has been instrumental in the development of several drugs today in the market. Computational methods can also be used to elucidate the energies associated with chemical reactivity and predict how to improve a synthetic protocol. These two applications of computational medicinal chemistry is the focus of this thesis. In the first part of this work, qu

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31

Jahn, Andreas [Verfasser]. "Molecular Flexibility Encodings for Virtual Screening and Machine Learning / Andreas Jahn." München : Verlag Dr. Hut, 2012. http://d-nb.info/1026652324/34.

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32

Santos, Alan Diego dos. "Ranking ligands in structure-based virtual screening using siamese neural networks." Pontif?cia Universidade Cat?lica do Rio Grande do Sul, 2017. http://tede2.pucrs.br/tede2/handle/tede/7763.

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33

Xiang, Hua. "Similarity-based virtual screening : effect of the choice of similarity measure." Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/5662/.

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The aim of the research was to identify novel similarity measures for similarity-based virtual screening. Similarity-based virtual screening is at the lead identification stage of drug discovery process and normally requires explorations in large scale databases. Thus, the improvement of accuracy of the methods employed could result in a significant enhancement of effectiveness of the whole process of drug discovery. There are three key components involved in similarity-based virtual screening, i.e., structural representations, similarity coefficients and weighting schemes. The research focuse

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34

Almeida, Jonathan Resende de. "Estudos de modelagem molecular e relação estrutura-atividade da acetilcolinesterase e inibidores em Mal de Alzheimer." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/60/60136/tde-21032011-102116/.

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O Mal de Alzheimer é a causa mais importante de demência em idosos. A progressão dos sintomas da doença está associada com modificações estruturais nas sinapses colinérgicas em determinadas regiões cerebrais e, consequentemente, à diminuição do potencial de neurotransmissão colinérgica. Desta forma, o aumento da capacidade de neurotransmissão colinérgica constitui o mecanismo fundamental dos fármacos utilizados para o tratamento do Mal de Alzheimer. Atualmente, o único tratamento clínico eficaz para o Mal de Alzheimer (MA) é a utilização de inibidores da acetilcolinesterase (AChE). Os anticol

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35

Totrov, Maxim. "Computational studies on protein-ligand docking." Thesis, Open University, 1999. http://oro.open.ac.uk/58005/.

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This thesis describes the development and refinement of a number of techniques for molecular docking and ligand database screening, as well as the application of these techniques to predict the structures of several protein-ligand complexes and to discover novel ligands of an important receptor protein. Global energy optimisation by Monte-Carlo minimisation in internal co-ordinates was used to predict bound conformations of eight protein-ligand complexes. Experimental X-ray crystallography structures became available after the predictions were made. Comparison with the X-ray structures showed

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36

Evans, Matthew Darold. "Drug candidate discovery by high-throughput virtual screening of protein binding sites /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2006. http://uclibs.org/PID/11984.

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37

Ren, Xin. "Quantitative structure-activity relationship based virtual screening for novel androgen receptor antagonists." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/43293.

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Androgen receptor (AR) plays a critical role in prostate cancer development and progression. All current therapeutic AR inhibitors modulate the receptor via direct binding to its Hormone Binding Site (HBS). Despite the identification of other small molecule binding areas on the AR surface including Activation Function 2 (AF2), binding function 3 (BF3), and N-terminal domain (NTD), HBS continues to be the major target site for AR antagonists (even though this site is prone to resistant mutations). Thus, there is a high need for the identification and development of novel antagonists targeting H

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38

Kirtay, Chrysi. "Development and application of a knowledge-based scoring function for virtual screening." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612957.

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39

Malvezzi, Alberto. "Modelos de virtual Screening de inibidores da cruzaína: desenvolvimento e validação experimental." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/46/46135/tde-10082016-115529/.

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Com o objetivo de buscar e identificar novo(s) inibidor(es) da cruzaína uma cisteíno-protease do Trypanosoma cruzi, o agente etiológico da doença de Chagas foram propostos, validados e, a seguir, aplicados sobre a biblioteca de compostos ZINC (3.294.714 compostos), dois modelos de virtual screening (Modelos I e II). Os modelos de virtual screening propostos, contendo seqüências de filtros físicoquímicos, farmacofóricos, de docking e de seleção por inspeção visual, foram construídos a partir de informações de 13 complexos da cruzaína e de 20 complexos de outras cisteínoprotease, cujas estrutu

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40

Alaasam, Mohammed. "Identification of novel monoamine oxidase B inhibitors from ligand based virtual screening." Kent State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=kent1405439915.

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41

Buonfiglio, Rosa <1985&gt. "Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6330/1/Tesi_Buonfiglio.pdf.

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The dynamic character of proteins strongly influences biomolecular recognition mechanisms. With the development of the main models of ligand recognition (lock-and-key, induced fit, conformational selection theories), the role of protein plasticity has become increasingly relevant. In particular, major structural changes concerning large deviations of protein backbones, and slight movements such as side chain rotations are now carefully considered in drug discovery and development. It is of great interest to identify multiple protein conformations as preliminary step in a screening campaign. Pr

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Buonfiglio, Rosa <1985&gt. "Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6330/.

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The dynamic character of proteins strongly influences biomolecular recognition mechanisms. With the development of the main models of ligand recognition (lock-and-key, induced fit, conformational selection theories), the role of protein plasticity has become increasingly relevant. In particular, major structural changes concerning large deviations of protein backbones, and slight movements such as side chain rotations are now carefully considered in drug discovery and development. It is of great interest to identify multiple protein conformations as preliminary step in a screening campaign. Pr

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43

Pham, Minh Quan. "Bio-pharmacological screening on liver-protective and anti-hepatocarcinoma activities of Vietnam natural products." Thesis, Toulouse 3, 2016. http://www.theses.fr/2016TOU30042/document.

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Le carcinome hépatocellulaire (HCC) est le cancer du foie le plus répandu et représente la seconde cause de décès par cancer dans le monde. Un mauvais pronostic et l'absence de traitement efficace en font un problème majeur de santé publique dans les pays en voie de développement, notamment en Asie du Sud-Est, justifiant pleinement la recherche de molécules ou d'approches thérapeutiques nouvelles contre l'HCC. Ce travail porte sur la recherche de molécules isolées de plantes vietnamiennes actives contre l'HCC. La première approche a consisté en un criblage pharmacologique de 33 substances natu

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44

Araújo, Sergio Xavier Barbosa. "Virtual screening de possíveis inibidores da trans-enoil-ACP-redutase de Mycobacterium tuberculosis." reponame:Repositório Institucional da UFC, 2013. http://www.repositorio.ufc.br/handle/riufc/15014.

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ARAÚJO, S. X. B. Virtual screening de possíveis inibidores da trans-enoil-ACP-redutase de Mycobacterium tuberculosis. 2013. 130 F. Tese (Doutorado em Química) - Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2013<br>Submitted by Daniel Eduardo Alencar da Silva (dealencar.silva@gmail.com) on 2014-11-28T20:10:04Z No. of bitstreams: 1 2013_tese_sxbaraujo.pdf: 3669672 bytes, checksum: bc41b0086c3cf3c170bb2831b63361b6 (MD5)<br>Approved for entry into archive by José Jairo Viana de Sousa(jairo@ufc.br) on 2016-01-29T19:57:14Z (GMT) No. of bitstreams: 1 2013_tese_sxbaraujo.pdf: 366967

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Urbaczek, Sascha [Verfasser], and Matthias [Akademischer Betreuer] Rarey. "A consistent cheminformatics framework for automated virtual screening / Sascha Urbaczek. Betreuer: Matthias Rarey." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2015. http://d-nb.info/1072553724/34.

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46

Heikamp, Kathrin [Verfasser]. "Application and Development of Computational Methods for Ligand-Based Virtual Screening / Kathrin Heikamp." Bonn : Universitäts- und Landesbibliothek Bonn, 2014. http://d-nb.info/1052061036/34.

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47

Montemurro, Luca Antonio <1977&gt. "Virtual screening di inibitori del complesso N-Myc/Max e valutazioni in vitro." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/1070/1/Tesi_Montemurro_Luca.pdf.

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Montemurro, Luca Antonio <1977&gt. "Virtual screening di inibitori del complesso N-Myc/Max e valutazioni in vitro." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/1070/.

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49

Gregori, Puigjané Elisabet. "A new Ligand-Based approach to virtual screening, and prolifing or large chemical libraries." Doctoral thesis, Universitat Pompeu Fabra, 2008. http://hdl.handle.net/10803/7166.

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La representació de les molècules per mitjà de descriptors moleculars és la base de moltes de les eines computacionals pel disseny de fàrmacs. Aquests mètodes computacionals es basen en l'abstracció de l'estructura química per resumir aquelles característiques rellevants sent al mateix temps eficients en la comparació de grans llibreries de molècules. Una característica molt important d'aquests descriptors és la seva habilitat de capturar la informació rellevant per la interacció amb qualsevol proteïna independentment de l'esquelet del compost. Això permet detectar com a similars qualsevol pa

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50

Tunca, Guzin. "A virtual screening procedure combining pharmacophore filtering and molecular docking with the LIE method." Doctoral thesis, Universitat Autònoma de Barcelona, 2012. http://hdl.handle.net/10803/284031.

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Actualment, el cribratge virtual juga un paper central en el món del descobriment de fàrmacs. L’anàlisi in silico permet el cribatge de milions de molècules petites i la tria de les més prometedores per a les proves experimentals. Per trobar candidats que puguin esdevenir fàrmacs, és crucial reunir una sèrie d’eines computacionals individuals i complementàries. En aquesta tesi, es descriu un procediment automatitzat de cribatge virtual que combina el modelat de farmacòfors i el seu ús en cerques, mètodes d’alt rendiment d’acoblament molecular, puntuació de consens i estimació d'energia lliure

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