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Dissertations / Theses on the topic 'Molecular docking'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Iakovou, Georgios. "Simulating molecular docking with haptics." Thesis, University of East Anglia, 2015. https://ueaeprints.uea.ac.uk/59468/.

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Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow the study of the binding process. In molecular docking, haptics enables the user to sense the interaction forces and intervene cognitively in the docking process. Haptics-assisted docking systems provide an immersive virtual docking environment where the user can interact with the molecules, feel the interaction forces using their sense of touch, identify visually

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2

Atkovska, Kalina, Sergey A. Samsonov, Maciej Paszkowski-Rogacz, and M. Teresa Pisabarro. "Multipose Binding in Molecular Docking." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-147177.

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Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e.,

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3

Landaverde, Raphael J. "GPU optimizations for a production molecular docking code." Thesis, Boston University, 2014. https://hdl.handle.net/2144/21199.

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Thesis (M.Sc.Eng.) -- Boston University<br>Scientists have always felt the desire to perform computationally intensive tasks that surpass the capabilities of conventional single core computers. As a result of this trend, Graphics Processing Units (GPUs) have come to be increasingly used for general computation in scientific research. This field of GPU acceleration is now a vast and mature discipline. Molecular docking, the modeling of the interactions between two molecules, is a particularly computationally intensive task that has been the subject of research for many years. It is a critica

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4

De, Youngster Dela. "An Isometry-Invariant Spectral Approach for Macro-Molecular Docking." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30226.

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Proteins and the formation of large protein complexes are essential parts of living organisms. Proteins are present in all aspects of life processes, performing a multitude of various functions ranging from being structural components of cells, to facilitating the passage of certain molecules between various regions of cells. The 'protein docking problem' refers to the computational method of predicting the appropriate matching pair of a protein (receptor) with respect to another protein (ligand), when attempting to bind to one another to form a stable complex. Research shows that matching th

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5

Tantar, Alexandru-Adrian. "Hybrid parallel metaheuristics for molecular docking on computational grids." Thesis, Lille 1, 2009. http://www.theses.fr/2009LIL10166.

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Cette thèse porte sur les méta-heuristiques hiérarchiques parallèles adaptatives pour l'échantillonnage conformationnel. Étant un problème hautement combinatoire et multlmodal, l'échantillonnage conformationnel requière la construction d'approches hybrides à large échelle. Après une analyse dei modèles mathématiques, nécessitant l'examen des différentes formulations du champ de force, nous avons proposé une étude des opérateurs de variation et des méthodes de recherche locale adaptés au problème ainsi que leur hybridation dynamique et adaptative. Cette étude nous a conduit à la proposition de

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6

BASCIU, ANDREA. "An enhanced-sampling MD-based protocol for molecular docking." Doctoral thesis, Università degli Studi di Cagliari, 2020. http://hdl.handle.net/11584/284135.

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Understanding molecular recognition of small molecules by proteins in atomistic detail is key for drug design. Molecular docking is a widely used computational method to mimic ligand-protein association in silico. However, predicting conformational changes occurring in proteins upon ligand binding is still a major challenge. Ensemble docking approaches address this issue by considering a set of different conformations of the protein obtained either experimentally or from computer simulations, e.g. from molecular dynamics. However, holo structures prone to host (the correct) ligands are

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7

DI, DOMIZIO ALESSANDRO. "Development of methodologies for molecular docking and their applications." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2009. http://hdl.handle.net/10281/7460.

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Virtual High Throughput Screening (vHTS) has an increasingly important role in lowering both costs and time in drug discovery. The present work deals with the development (C++ programming language) of a new molecular docking software (semi-flexible model) to be used for vHTS. It would improve some of the main aspects of this type of softwares in current use, with particular reference to the program AutoDock: a particular importance is given to the calculation of the ligand conformational energy variation in passing from the unbound to the bound state, which represents a crucial term in the doc

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8

Boyce, Sarah Emily. "Model systems for molecular docking: Understanding molecular recognition in polar and charged binding sites." 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:3390113.

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9

Salmaso, Veronica. "Exploring protein flexibility during docking to investigate ligand-target recognition." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421817.

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Ligand-protein binding models have experienced an evolution during time: from the lock-key model to induced-fit and conformational selection, the role of protein flexibility has become more and more relevant. Understanding binding mechanism is of great importance in drug-discovery, because it could help to rationalize the activity of known binders and to optimize them. The application of computational techniques to drug-discovery has been reported since the 1980s, with the advent computer-aided drug design. During the years several techniques have been developed to address the protein flexibil

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10

Genheden, Samuel. "A fast protein-ligand docking method." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-69.

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<p>In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biologic

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11

Daldrop, Peter. "Structure and molecular recognition in riboswitches." Thesis, University of Dundee, 2011. https://discovery.dundee.ac.uk/en/studentTheses/db338d42-75c1-43a6-be6a-11399f04989e.

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Riboswitches are cis-acting gene regulatory RNAs, which function without involvement of proteins. They have been implicated as drug targets and are attractive systems for the study of RNA-ligand binding and RNA folding. The purine riboswitch was used as a model system for RNA-ligand docking. Published binding data was successfully reproduced in silico and compounds predicted to bind the riboswitch in a virtual screening were tested experimentally. Structural data confirming the predicted binding mode for several cases was obtained. The problems encountered were not specific to RNA-ligand docki

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12

Alisaraie, Laleh. "Improvement of a molecular docking approach and its applications using QXP+." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=985169141.

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13

Sparring, Leonard. "Conquering Chemical Space : Optimization of Docking Libraries through Interconnected Molecular Features." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416977.

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Copied selected text to selection primary: The development of new pharmaceuticals is a long and ardous process that typically requires more than 10 years from target identification to approved drug. This process often relies on high throughput screening of molecular libraries. However, this is a costly and time-intensive approach and the selection of molecules to screen is not obvious, especially in relation to the size of chemical space, which has been estimated to consist of 10 60 compounds. To accelerate this exploration, molecules can be obtained from virtual chemical libraries and tested

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14

VERTEMARA, JACOPO. "Computational modelling of macromolecules: prediction of the 3-D structure, catalytic activity and dynamic features of proteins." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2018. http://hdl.handle.net/10281/198948.

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Durante il mio PhD ho utilizzato diverse tecniche computazionali, in particolare metodi QM e MM, per studiare la relazione struttura/attività delle proteine. Il primo progetto consiste nella caratterizzazione strutturale del cofattore metallico FeMo-co presente nel sito attivo delle Mo-nitrogenasi. L'obbiettivo è studiare da un punto di vista strutturale l'intermedio E 4 che è attualmente ritenuto essere lo step nel quale avviene il legame con N 2 . A tale scopo sono state svolte simulazioni DFT sul FeMo-co considerando ogni possibile stato redox dei ferri proposto in letteratura ( [5FeIII:2F

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15

Lima, Karine Thiers Leitão. "Polimorfismos do gene da plastoquinol oxidase (PTOX) em ecotipos de Arabidopsis thaliana (projeto 1001 genomas): correlações de expressão gênica e de variantes estruturais da proteína com a distribuição geográfica dos ecotipos." reponame:Repositório Institucional da UFC, 2017. http://www.repositorio.ufc.br/handle/riufc/22414.

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LIMA, Karine Thiers Leitão. Polimorfismos do gene da plastoquinol oxidase (PTOX) em ecotipos de Arabidopsis thaliana (projeto 1001 genomas): correlações de expressão gênica e de variantes estruturais da proteína com a distribuição geográfica dos ecotipos. 2017. 110 f. Dissertação (Mestrado em Bioquímica)-Universidade Federal do Ceará, Fortaleza, 2017.<br>Submitted by Jairo Viana (jairo@ufc.br) on 2017-03-28T19:52:31Z No. of bitstreams: 1 2017_dis_ktllima.pdf: 4068096 bytes, checksum: f6b3738f233a7c99cf008ea14382bf0d (MD5)<br>Approved for entry into archive by Jairo Viana (jairo@ufc.br) on 2017

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RABELLO, Marcelo Montenegro. "Comparação metodológica de abordagens in silico no estudo de moléculas antiofídicas através de sua ação em toxinas isoladas de venenos de serpentes." Universidade Federal de Pernambuco, 2012. https://repositorio.ufpe.br/handle/123456789/18486.

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Submitted by Caroline Falcao (caroline.rfalcao@ufpe.br) on 2017-04-04T19:45:56Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) 2012-Dissertação-MarceloRabello.pdf: 28475883 bytes, checksum: a9615b2d4a3b20d9263dba3af92c324c (MD5)<br>Made available in DSpace on 2017-04-04T19:45:56Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) 2012-Dissertação-MarceloRabello.pdf: 28475883 bytes, checksum: a9615b2d4a3b20d9263dba3af92c324c (MD5) Previous issue date: 2012<br>Este projeto pode ser resumido como

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Silva, Luciane Sussuchi da [UNESP]. "Estudos computacionais de esfingomielinases D: docking, dinâmica molecular e métodos híbridos QM/MM." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/139389.

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Made available in DSpace on 2016-06-07T17:12:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-09-29. Added 1 bitstream(s) on 2016-06-07T17:17:05Z : No. of bitstreams: 1 000864119_20161015.pdf: 820535 bytes, checksum: 8cfc04e894aa886137e9ca9b9cd3aae0 (MD5) Bitstreams deleted on 2016-10-17T11:54:15Z: 000864119_20161015.pdf,. Added 1 bitstream(s) on 2016-10-17T11:54:54Z : No. of bitstreams: 1 000864119.pdf: 2517185 bytes, checksum: f66c5ecaac1008f20a8256cf9a4604ed (MD5)<br>Esfingomielinase D (SMase D) é uma enzima conhecida por catalisar a clivagem de esfingomielina em ceramida-1-fosf

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Silva, Luciane Sussuchi da. "Estudos computacionais de esfingomielinases D : docking, dinâmica molecular e métodos híbridos QM/MM /." São José do Rio Preto, 2015. http://hdl.handle.net/11449/139389.

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Orientador: Jorge Chahine<br>Banca: Ronaldo Júnio De Oliveira<br>Banca: José Fernando Ruggiero Bachega<br>Banca: Gabriel Gouvêa Slade<br>Banca: Fábio Rogério de Moraes<br>Resumo: Esfingomielinase D (SMase D) é uma enzima conhecida por catalisar a clivagem de esfingomielina em ceramida-1-fosfato e colina, atividade presente apenas em aranhas do gênero Loxosceles (aranhas marrom) e em bactérias patogênicas do tipo Corynebacterium. A SMase D, também encontrada na literatura como fosfolipase D, é o principal componente do veneno de aranhas do gênero Loxosceles, capaz de induzir sozinha as lesões d

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19

Andersson, David. "Multivariate design of molecular docking experiments : An investigation of protein-ligand interactions." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-35736.

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To be able to make informed descicions regarding the research of new drug molecules (ligands), it is crucial to have access to information regarding the chemical interaction between the drug and its biological target (protein). Computer-based methods have a given role in drug research today and, by using methods such as molecular docking, it is possible to investigate the way in which ligands and proteins interact. Despite the acceleration in computer power experienced in the last decades many problems persist in modelling these complicated interactions. The main objective of this thesis was t

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20

Maganhi, Stella Hernandez. "Telurooxetanas : estudos cristalográficos, modelagem molecular e cálculos de docking para aplicação biológica." Universidade Federal de São Carlos, 2009. https://repositorio.ufscar.br/handle/ufscar/6445.

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Made available in DSpace on 2016-06-02T20:36:21Z (GMT). No. of bitstreams: 1 2240.pdf: 3981938 bytes, checksum: ce9575f4d9edde7a78432d592db4dd5a (MD5) Previous issue date: 2009-02-10<br>Universidade Federal de Minas Gerais<br>This work is composed of 4 chapters. In Chapter 1 is a description of the problems addressed here, starting with the characteristics of the protein, its biological and social importance, and the interactions responsible for both its structure and the formation of ligand-protein complexes, there is also a brief description of Te(IV) compounds followed by the presentation

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Frantz, F?bio Andr? "Smart execution of molecular docking simulations of a fully-flexible receptor model." Pontif?cia Universidade Cat?lica do Rio Grande do Sul, 2012. http://tede2.pucrs.br/tede2/handle/tede/5177.

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Made available in DSpace on 2015-04-14T14:49:48Z (GMT). No. of bitstreams: 1 439095.pdf: 3289381 bytes, checksum: eb6fc534e5a9d631dbafb97aa0a9c407 (MD5) Previous issue date: 2012-04-12<br>Molecular docking simulations of Fully-Flexible Receptor (FFR) models are coming of age. However, they demand parallelization of computing activities for their executions and generate huge amounts of data that needs to be analyzed. Many Task Computing (MTC) is an attractive paradigm routinely applied to execute intensive tasks. In this work we propose an environment to execute molecular docking simulations

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22

Vianna, Carolina Pasa. "Identificação de ligantes da chiquimato quinase de Mycobacterium tuberculosis por docking molecular." Pontifícia Universidade Católica do Rio Grande do Sul, 2011. http://hdl.handle.net/10923/1377.

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Made available in DSpace on 2013-08-07T18:41:52Z (GMT). No. of bitstreams: 1 000431138-Texto+Completo-0.pdf: 1089028 bytes, checksum: b3d0bb2ab98885aab405ecc4329e3335 (MD5) Previous issue date: 2011<br>Tuberculosis (TB) is the major cause of human mortality from a curable infectious disease, attacking mainly in developing countries. Among targets identified in Mycobacterium tuberculosis genome, enzymes of the shikimate pathway deserve special attention, since they are essential to the survival of the microorganism and absent in mammals. The object of our study is shikimate kinase (SK), the f

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23

Frantz, Fábio André. "Smart execution of molecular docking simulations of a fully-flexible receptor model." Pontifícia Universidade Católica do Rio Grande do Sul, 2012. http://hdl.handle.net/10923/1544.

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Made available in DSpace on 2013-08-07T18:42:49Z (GMT). No. of bitstreams: 1 000439095-Texto+Completo-0.pdf: 3289381 bytes, checksum: eb6fc534e5a9d631dbafb97aa0a9c407 (MD5) Previous issue date: 2012<br>Molecular docking simulations of Fully-Flexible Receptor (FFR) models are coming of age. However, they demand parallelization of computing activities for their executions and generate huge amounts of data that needs to be analyzed. Many Task Computing (MTC) is an attractive paradigm routinely applied to execute intensive tasks. In this work we propose an environment to execute molecular dockin

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24

BORDOGNA, ANNALISA. "Predicting the binding modes of protein complexes: new strategies for molecular docking." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/19617.

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Docking approaches and homology modelling procedures have recently become protagonists in the structural prediction of protein complexes. Therefore, in the last years it raised the need of developing more and more reliable tools and defining some guidelines to obtain accurate prediction of those structures. These goals are particularly relevant when only poorly accurate information about the proteins or the interaction (e.g. no interface indication for protein-protein docking, or protein models instead of experimental structures) is available. In this thesis several strategies based on combin

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25

Ismail, Alexandre. "Molecular modeling of Coq6, a ubiquinone biosynthesis flavin-dependent hydroxylase. Evidence of a substrate access channel." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066044/document.

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Coq6 est une enzyme impliquée dans la biosynthèse du coenzyme Q (aussi nommé ubiquinone, ou Q), un lipide benzoquinone polyprenylé essentiel à la fonction de la chaîne respiratoire mitochondriale. Dans la levure Saccharomyces cerevisiae, cette monooxygénase flavine-dépendante putatif est proposé pour hydroxyler le noyau benzénique d' un précurseur du coenzyme Q à la position C5. Nous montrons ici à travers des études biochimiques que Coq6 est une flavoprotéine utilisant le FAD comme cofacteur. Des modèles d'homologie du complexe Coq6-FAD ont étés réalisés et étudiés par dynamique moléculaire e

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26

Lock, Lisa S. "Recruitment specificity of Gab family docking proteins and implications for MET receptor-mediated epithelial morphogenesis." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=82919.

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Activation of cell-surface receptors by extracellular signals can generate distinct biological responses. Many of these signals are coordinated through docking proteins, including those in the Gab family (Gab1, Gab2 and Gab3). Following activation of receptor tyrosine kinases (RTKs), cytokine or antigen receptors, docking proteins are recruited to the receptor complex and become phosphorylated on tyrosine residues, providing binding sites for multiple proteins involved in signal transduction. In this manner, they act to diversify and localize signals downstream from receptors by virtue

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Nascimento, Alessandro Silva. "Interações dos receptores nucleares com seus ligantes: Estudos estruturais do receptor de hormônio tireoidiano, do receptor de mineralocorticóide e do receptor ativado por proliferadores peroxissomais." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/76/76132/tde-13032009-124546/.

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Os receptores nucleares constituem uma superfamília de fatores de transcrição regulados pela interação com hormônios. Esta superfamília inclui, por exemplo, os receptores de hormônio tireoidiano, estrogênio, androgênio, glicocorticóide e mineralocorticóide. Neste trabalho, empregamos técnicas de biologia estrutura e bioinformática para estudar as interações entre alguns dos membros da família de receptores nucleares e seus respectivos ligantes. Para o receptor de hormônio tireoidiano, foi demonstrado, através da análise das estruturas cristalográficas das duas isoformas do receptor ligados ao

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28

PAIOTTA, ALICE. "Synthesis of Glycoderivatives as Molecular Tools in Medicinal Chemistry and Nano-Medicinal Chemistry." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2018. http://hdl.handle.net/10281/199137.

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Durante il terzo anno di dottorato mi sono occupata della sintesi finale dei glicomimetici del substrato naturale dell’enzima AGM1 GlcNAc-6P o del prodotto GlcNAc-1P. Le sintesi messe a punto sono necessarie per ottenere prodotti finali utilizzabili come strumenti molecolari chimici per studiare il ruolo dell’HBP nella regolazione della proliferazione e la sopravvivenza delle cellule tumorali. I prodotti presentati (caratterizzati mediante NMR (1H. COSY, HSQC e 13C) e Massa) sono stati preparati protetti (acetilati sugli ossidrili) per i test cellulari per favorire la loro diffusione attr

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Das, Biswajit. "Qsar analysis, docking & molecular dynamics simulation of several antimicrobial compounds and receptors." Thesis, University of North Bengal, 2015. http://ir.nbu.ac.in/handle/123456789/1525.

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Galanis, Alex. "Molecular mechanisms of signalling specificity to the transcription factor SAP-1." Thesis, University of Newcastle Upon Tyne, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327230.

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Ullmann, G. Matthias. "Simulation and analysis of docking and molecular dynamics of electron transfer protein complexes." [S.l. : s.n.], 1998. http://darwin.inf.fu-berlin.de/1998/23/index.html.

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Trindade, Antonio Carlos. "Estudo cristalino, molecular, supramolecular e de \" Docking\" de alguns compostos derivados de quinonas." Universidade de São Paulo, 2006. http://www.teses.usp.br/teses/disponiveis/46/46132/tde-16052007-140758/.

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Neste trabalho são apresentados os resultados das determinações cristalinas, estruturais e supramoleculares, por difração de raio X, bem como os estudos de \"docking\" , de oito compostos derivados da 1,4-quinona. As estruturas resolvidas e refinadas mostraram a existência de ligações de hidrogênio, não convencionais intra e intermoleculares. Estas últimas permitiram entender o empacotamento cristalino em cada composto. Os resultados cristalográficos foram comparados com aqueles encontrados na literatura. Mas as estruturas correspondentes aos compostos AC1 (6,7-bis-fenilsulfanil-1,4-dihidro-1

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Vianna, Carolina Pasa. "Identifica??o de ligantes da chiquimato quinase de Mycobacterium tuberculosis por docking molecular." Pontif?cia Universidade Cat?lica do Rio Grande do Sul, 2011. http://tede2.pucrs.br/tede2/handle/tede/5389.

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Made available in DSpace on 2015-04-14T14:51:05Z (GMT). No. of bitstreams: 1 431138.pdf: 1089028 bytes, checksum: b3d0bb2ab98885aab405ecc4329e3335 (MD5) Previous issue date: 2011-03-10<br>Entre as doen?as infecciosas, a tuberculose se destaca, como sendo a principal causa de morte humana, principalmente em pa?ses em desenvolvimento. Entre os alvos identificados no genoma de Mycobacterium tuberculosis, as enzimas da via do chiquimato merecem aten??o especial, pois s?o essenciais para a sobreviv?ncia dos microorganismos e ausente em mam?feros. O objeto do nosso estudo ? a quinta enzima desta v

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Tanczos, Anna Carroll. "Investigations of two distinct pharmacologically relevant proteins using docking studies and molecular dynamics." Thesis, University of Surrey, 2004. http://epubs.surrey.ac.uk/844408/.

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Docking of a flexible ligand to a rigid protein, followed by molecular dynamics (MD) studies to allow movement of the protein is shown to be a useful method for investigating pharmacologically relevant interactions. Studies of MMB lectins (beta-sheet proteins with shallow binding sites) reveal the importance of dimerisation to the activation of all of the carbohydrate binding sites of these lectins, finalising site III into a shape that can accommodate mannose. Aloe lectin was shown to have the overall fold of a MMB lectin and to be capable of forming a dimeric unit, shown to be stable using M

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Fernandes, Claudia Lemelle. "Modelagem molecular e estudos de docking da enzima corismato sintase de Mycobacterium tuberculosis." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2006. http://hdl.handle.net/10183/8453.

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As enzimas da via do ácido chiquímico constituem um excelente alvo para o desenho de novos agentes antibacterianos. Esta rota é encontrada em bactérias, fungos, plantas e parasitas do filo apicomplexa, mas está ausente em mamíferos. A Corismato sintase (CS) catalisa o último passo desta rota, produto que é utilizado em outras reações biossintéticas, como biossíntese de aminoácidos aromáticos, folato, vitamina K e ubiquinona. Esta reação é a mais incomum de toda rota e é unica na natureza. Ela converte 5-enolpiruvil-chiqiuimato-3-fosfato (EPSP) em corismato na presença de uma flavina mononucleo

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Mendes, Josiane Enevina. "Docking de herbicidas na glutationa transferase tau4-4 de soja (Glycine max)." Universidade Federal de São Carlos, 2011. https://repositorio.ufscar.br/handle/ufscar/6974.

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Made available in DSpace on 2016-08-17T18:39:37Z (GMT). No. of bitstreams: 1 3640.pdf: 5869617 bytes, checksum: 4643e7ab6ff128afd74bd3d51d8588f3 (MD5) Previous issue date: 2011-03-30<br>Financiadora de Estudos e Projetos<br>This study, based on molecular docking, describes the search for the most favorable conformations when complexes between herbicides, used in soybean cultivation, and an enzyme involved in the detoxification process are formed and based on these results some guidelines for the developing of new compounds are proposed. The glutathione transferase Tau, GmGSTU4-4, from soybea

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Kinkel, Katrin. "Prediction of the binding mode of suberone-inhibitors in the p38 MAP kinase with molecular modeling studies." [S.l. : s.n.], 2008.

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Baptistini, Natália. "Análise in silico, in vitro e in vivo de compostos organocalcogênios como possíveis anti-inflamatórios." Universidade Federal de São Carlos, 2015. https://repositorio.ufscar.br/handle/ufscar/7554.

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Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2016-09-27T12:14:06Z No. of bitstreams: 1 TeseNB.pdf: 25264059 bytes, checksum: f823e6e565d3555a5d49056afd7c39fe (MD5)<br>Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T20:08:42Z (GMT) No. of bitstreams: 1 TeseNB.pdf: 25264059 bytes, checksum: f823e6e565d3555a5d49056afd7c39fe (MD5)<br>Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T20:08:48Z (GMT) No. of bitstreams: 1 TeseNB.pdf: 25264059 bytes, checksum: f823e6e565d3555a5d49056afd7c39fe (MD5)<br>Made avail

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Canto, Vanessa Petry do. "Estudo computacional das monoaminoxidases A e B com substratos e inibidores." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2014. http://hdl.handle.net/10183/97873.

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A monoaminoxidase (MAO) é uma enzima importante, que pode atuar como alvo terapêutico. Inibidores da MAO-A apresentam atividade no tratamento de distúrbios de humor, enquanto os inibidores seletivos da MAO-B tem uso, especialmente, no tratamento da Doença de Parkinson. O conhecimento das interações ENZIMA-INIBIDOR é importante no planejamento de fármacos. Nesse contexto, foram realizados estudos das enzimas MAO-A e MAO-B com diferentes ligantes, através da combinação das metodologias de docking, Dinâmica Molecular e Ensemble Docking. Foram escolhidos os ligantes derivados da 1,4-naftoquinona (

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Shimo, Helder Ken. "Auto-organização da população em sistemas imunológicos artificiais aplicada ao docking de proteínas." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-30082012-161501/.

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Vários problemas do mundo real podem ser analisados como problemas de otimização. Na bioinformática, em especial, como exemplos podem ser citados o alinhamento múltiplo de sequências, a filogenia, a predição de estruturas de proteínas e RNA, entre outros. As Meta-heurísticas Populacionais (MhP) são técnicas baseadas em interações de conjuntos de soluções candidatas, como elementos de uma população, utilizadas na otimização de funções. Seu uso é especialmente interessante na otimização de problemas onde há conhecimento parcial ou nenhum do espaço de busca. O objetivo deste trabalho é investigar

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Leis, Simon [Verfasser], Martin [Akademischer Betreuer] Zacharias, and Iris [Akademischer Betreuer] Antes. "Impact of Protein conformational Changes on Molecular Docking - Design of a Docking Approach including Receptor Flexibility / Simon Leis. Gutachter: Iris Antes. Betreuer: Martin Zacharias." München : Universitätsbibliothek der TU München, 2012. http://d-nb.info/1030099464/34.

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RABELLO, Marcelo Montenegro. "Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica." Universidade Federal de Pernambuco, 2016. https://repositorio.ufpe.br/handle/123456789/17588.

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Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2016-07-29T17:57:19Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) MMR-TESE.pdf: 16044503 bytes, checksum: 1c3b4963930b3b75a91e718bd1893e50 (MD5)<br>Made available in DSpace on 2016-07-29T17:57:19Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) MMR-TESE.pdf: 16044503 bytes, checksum: 1c3b4963930b3b75a91e718bd1893e50 (MD5) Previous issue date: 2016-02-29<br>Facepe<br>Este trabalho apresenta uma metodologia in silico para o estudo

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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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Leves, Natalia. "Nanopartículas de grafite para carreamento de antiinflamatórios não esteroidais por estudos de docking molecular." Universidade Federal de São Carlos, 2013. https://repositorio.ufscar.br/handle/ufscar/7035.

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Made available in DSpace on 2016-08-17T18:39:50Z (GMT). No. of bitstreams: 1 6068.pdf: 11514210 bytes, checksum: 8c9214a7a0368fd3be3320eb3e04318d (MD5) Previous issue date: 2013-08-13<br>The non steroidal anti-inflammatory drugs have been known for over 100 years and has been widely used by mankind. However cause adverse effects, since gastrointestinal complications to cardiac diseases many of these symptoms related to its nonspecific action in biological systems. Thus, the proposal of a drug delivery system for loading these drugs to the site of inflammation, could reduce these unwanted eff

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Fernandes, Vinícius Alves. "Ação do colesterol sobre a arquitetura da cromatina : docking molecular do colesterol ao nucleossomo." reponame:Repositório Institucional da UnB, 2010. http://repositorio.unb.br/handle/10482/21454.

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Dissertação (mestrado)—Universidade de Brasília, Faculdade de Ciências da Saúde, Programa de Pós-Graduação em Ciências Farmacêuticas, 2016.<br>Submitted by Camila Duarte (camiladias@bce.unb.br) on 2016-09-12T19:56:50Z No. of bitstreams: 1 2016_ViníciusAlvesFernandes.pdf: 4594049 bytes, checksum: 48f78b5328fa30fbeae24f268a04373c (MD5)<br>Approved for entry into archive by Raquel Viana(raquelviana@bce.unb.br) on 2016-09-20T21:41:03Z (GMT) No. of bitstreams: 1 2016_ViníciusAlvesFernandes.pdf: 4594049 bytes, checksum: 48f78b5328fa30fbeae24f268a04373c (MD5)<br>Made available in DSpace on 2016-09-2

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Sasi, Abd-Alkarim Nour-Addin. "Cardiovascular effects, molecular docking and chemo informatics analysis of compounds isolated from leonotis leonurus." Thesis, University of the Western Cape, 2015. http://hdl.handle.net/11394/5342.

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>Magister Scientiae - MSc<br>Leonotis leonurus (L. Leonurus) has relatively abundant diterpenes and has been used as a traditional herbal medicine for treating several ailments including influenza, muscular cramps, skin related diseases, menstrual, antilipidemic, hyperglycaemia and hypertension. In this study, diterpenoid compounds such as; Dubiin, SaponifiedDubiin, Hispanol, Marrubiin and DC9 were isolated from L. Leonurus plant. The cardiovascular effects of these isolated compounds were investigated in order to determine the response of anaesthetised normotensive Wistar rats (in-vivo) to th

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Grasel, Fábio dos Santos. "Investigação da interação de ligantes fluorescentes derivados de benzazóis com B-DNA por docking e dinâmica molecular." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2013. http://hdl.handle.net/10183/88548.

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Neste trabalho foi realizado o estudo por docagem e simulação de dinâmica molecular de doze derivados benzazólicos fluorescentes por ESIPT, interagindo com o dodecâmero de Dickerson-Drew na forma B-DNA. Estes doze ligantes foram divididos em dois grupos (A e B), sendo o primeiro grupo composto por derivados do 2-(2’-hidroxifenil)-benzoxazol e o segundo grupo composto por três derivados do 2-(4’-amino-2’-hidroxifenil)-benzazóis, alternando entre N, S e O no anel azólico, mais três bases de Tröger derivadas dos mesmos. Na análise da docagem molecular do grupo A, os derivados com grupamento –NH2

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Buldrini, Oviedo María Teresa. "Identificación de Potenciales Residuos Determinantes de Mayor Afinidad a Celulosa en una Endoglucanasa Mediante Estudios de Docking Molecular." Tesis, Universidad de Chile, 2012. http://repositorio.uchile.cl/handle/2250/104415.

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El bioetanol es un combustible complementario a las gasolinas, producido mediante fermentación de azúcares simples derivados de sacarosa, almidón o celulosa. Debido a su gran abundancia el material celulósico es particularmente atractivo como fuente de combustible. La hidrólisis de la celulosa puede realizase utilizando métodos químicos (ácidos o bases) o enzimáticos. La hidrólisis enzimática genera productos más puros y consume menos energía; sin embargo, debido a su bajo rendimiento se requiere usar grandes cantidades de enzima, lo cual eleva considerablemente los costos de producción. La

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Jiao, Wanting. "The Use of Molecular Modelling to Study Enzymic Action." Thesis, University of Canterbury. Department of Chemistry, 2011. http://hdl.handle.net/10092/6257.

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Molecular modelling has become widely used in chemistry and biology. The aim of this project is to use a range of molecular modelling techniques to study enzymic actions. This thesis consists of two parts. Part A of this thesis describes computational studies conducted for the calpain-calpastatin system. Calpain is a cysteine protease. Over-expression of calpain is associated with many diseases. Calpastatin is the naturally occurring specific regulator of calpain activity. In this part of the thesis, the dynamic conformational preferences of region B of the inhibitory domain in calpastatin we

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Silva, Viviane Aparecida. "Estudo, por modelagem molecular, da inibição da enzima acetohidroxiácido sintase utilizando diferentes derivados pirimidinilsalicilatos." Universidade Federal de Uberlândia, 2017. http://dx.doi.org/10.14393/ufu.di.2018.94.

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CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior<br>Herbicides inhibitors of the enzyme acetohydroxyacid synthase (AHAS) present high efficiency in the inhibitory activity with low doses of application and low toxicity for man and the environment. However, several weeds are getting resistence to some classes of herbicides, mainly in the case of AHAS group. Therefore, a proper computational planning of new bioactive compounds is crucial area to model new herbicides. In this study, the enzyme-herbicide interactions were analyzed from the analogous derivated of the pyrimidinyls

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