Auswahl der wissenschaftlichen Literatur zum Thema „Docking inverse“
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Zeitschriftenartikel zum Thema "Docking inverse"
Darme, Pierre, Manuel Dauchez, Arnaud Renard, Laurence Voutquenne-Nazabadioko, Dominique Aubert, Sandie Escotte-Binet, Jean-Hugues Renault, Isabelle Villena, Luiz-Angelo Steffenel und Stéphanie Baud. „AMIDE v2: High-Throughput Screening Based on AutoDock-GPU and Improved Workflow Leading to Better Performance and Reliability“. International Journal of Molecular Sciences 22, Nr. 14 (13.07.2021): 7489. http://dx.doi.org/10.3390/ijms22147489.
Der volle Inhalt der QuelleKammer, Daniel C., und Adam D. Steltzner. „Structural Identification of Mir Using Inverse System Dynamics and Mir/Shuttle Docking Data“. Journal of Vibration and Acoustics 123, Nr. 2 (01.12.2000): 230–37. http://dx.doi.org/10.1115/1.1355030.
Der volle Inhalt der QuelleKim, Stephanie S., Melanie L. Aprahamian und Steffen Lindert. „Improving inverse docking target identification with Z ‐score selection“. Chemical Biology & Drug Design 93, Nr. 6 (02.01.2019): 1105–16. http://dx.doi.org/10.1111/cbdd.13453.
Der volle Inhalt der QuellePerez, German, Marcello Mascini, Valentina Lanzone, Manuel Sergi, Michele Del Carlo, Mauro Esposito und Dario Compagnone. „Peptides Trapping Dioxins: A Docking-Based Inverse Screening Approach“. Journal of Chemistry 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/491827.
Der volle Inhalt der QuelleMa, Zhiwei, Xianjin Xu und Xiaoqin Zou. „MDockServer: An Efficient Docking Platform for Inverse Virtual Screening“. Biophysical Journal 114, Nr. 3 (Februar 2018): 56a. http://dx.doi.org/10.1016/j.bpj.2017.11.358.
Der volle Inhalt der QuelleXu, Xianjin, Marshal Huang und Xiaoqin Zou. „Docking-based inverse virtual screening: methods, applications, and challenges“. Biophysics Reports 4, Nr. 1 (Februar 2018): 1–16. http://dx.doi.org/10.1007/s41048-017-0045-8.
Der volle Inhalt der QuelleRusso, Silvana, und Walter Filgueira De Azevedo. „Advances in the Understanding of the Cannabinoid Receptor 1 – Focusing on the Inverse Agonists Interactions“. Current Medicinal Chemistry 26, Nr. 10 (20.06.2019): 1908–19. http://dx.doi.org/10.2174/0929867325666180417165247.
Der volle Inhalt der QuelleKamal, Ahmed A. M., Lucia Petrera, Jens Eberhard und Rolf W. Hartmann. „Structure–functionality relationship and pharmacological profiles of Pseudomonas aeruginosa alkylquinolone quorum sensing modulators“. Organic & Biomolecular Chemistry 15, Nr. 21 (2017): 4620–30. http://dx.doi.org/10.1039/c7ob00263g.
Der volle Inhalt der QuelleKämper, Andreas, Joannis Apostolakis, Matthias Rarey, Christel M. Marian und Thomas Lengauer. „Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies“. Journal of Chemical Information and Modeling 46, Nr. 2 (März 2006): 903–11. http://dx.doi.org/10.1021/ci050467z.
Der volle Inhalt der QuelleBan, Tomohiro, Masahito Ohue und Yutaka Akiyama. „Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem“. Computational Biology and Chemistry 73 (April 2018): 139–46. http://dx.doi.org/10.1016/j.compbiolchem.2018.02.008.
Der volle Inhalt der QuelleDissertationen zum Thema "Docking inverse"
Vasseur, Romain. „Développements HPC pour une nouvelle méthode de docking inverse : applications aux protéines matricielles“. Thesis, Reims, 2015. http://www.theses.fr/2015REIMS036.
Der volle Inhalt der QuelleThis work is a methodological and software development of so-called inverse molecular docking method. This method offers through an in house program AMIDE — Automatic Reverse Docking Engine — to distribute large numbers of molecular docking simulations on HPC architectures (com- puting clusters) with AutoDock 4.2 and AutoDock Vina applications. The principle of this method is to test small molecules on a set of potential target proteins. The program optimum parameters were defined from a pilot study and the protocol was validated on ligands and peptides binding MMPs and EBP extracellular matrix proteins. This method improves the conformational search in docking computation on experimental structures compared to existing protocols (blind docking). It is shown that the AMIDE program is more efficient to discriminate preferred binding sites in inverse proteins screening experiments than blind docking. These results are obtained by the implemen- tation of methods for partitioning the search space that also allow through a hybrid distribution system to deploy a set of independent embarassingly parallel tasks perfectly scalable
Cordonnier, Julien. „Toxoplasma gondii : identification par docking inverse sur des cibles moléculaires de composés actifs issus de ressources naturelles“. Electronic Thesis or Diss., Reims, 2024. http://www.theses.fr/2024REIMS001.
Der volle Inhalt der QuelleTree barks, by-product of forestry industry, constitute an abundant and sustainable source of natural compounds. Toxoplasma gondii is the parasite responsible for toxoplasmosis, posing a threat to fetuses, newborns, and immunocompromised individuals. The current therapeutics, limited and poorly tolerated, are now confronted to chemoresistant phenomena. This doctoral project aims to explore the chemical space associated with tree barks from the Champagne-Ardenne region, as relevant protein targets to fight T. gondii. An initial in silico evaluation using reverse docking (AMIDEv2.0) was carried out to identify biological target for triterpenes derived from betulone, isolated from the European alder, which had exhibited in vitro anti-toxoplasmosis activity. Among 87 proteins of T. gondii, CDPK3 was identified as the most probable target. Subsequently, a bank of 25 essential 3D protein structures for parasite survival, including 19 homology-modeled structures, was compiled. Thereafter, compounds from the Essential National Chemical Library were screened against this protein bank, using AMIDEv2.0. Two proteins were identified as potential targets; one of them was ATG3, a protein structure modeled from homologs with less than 50% identity. Subsequently, the barks of European Larch, whose n-heptane extract had shown significant activity (58% inhibition of parasitic growth at 100 µg/ml), were subjected to a chemical profiling. First, through a fractionation process using Centrifugal Partition Chromatography, and then a dereplication approach combining data from nuclear magnetic resonance and mass spectrometry. Tools like VersaDB and CATHEDRAL were developed to facilitate the creation of custom-databases and assess the confidence level of annotations. 52 molecules were annotated and associated with a confidence score. Simultaneously, in vitro tests demonstrated that 2 out of the 12 CPC fractions, primarily composed of terpenic derivatives, inhibited the parasite's survival by more than 40% at 25 µg/ml. Ultimately, the annotated compounds from L. decidua were subjected to AMIDEv2.0. The overlap between in vitro and in silico results highlighted 7-oxo-dehydroabietic acid and daniellic acid, strongly correlated with the in vitro inhibitory activity of the barks. CDPK1 and the SET-containing Protein are likely protein targets for these two ligands, thereby providing initial insights into their mechanism of action. These two hits are currently undergoing in vitro evaluation to verify the efficiency of developed approach during this doctoral project
Meslamani, Jamel-Eddine. „Développement de nouvelles méthodes de criblage in silico en chémogénomique“. Thesis, Strasbourg, 2012. http://www.theses.fr/2012STRAF009/document.
Der volle Inhalt der QuelleChemoinformatics and bioinformatics methods are now necessary in every drug discovery program. Pharmaceutical industries dedicate more than 10% of their research and development investment in computer aided drug design (Kapetanovic 2008). The emergence of these tools can be explained by the increasing availability of high performance calculating machines and also by the low cost of in silico analysis compared to in vitro tests.Biological tests that were performed over last decades are now a valuable source of information and a lot of databases are trying to list them. This huge amount of information led to the birth of a new research field called “chemogenomics”. The latter is focusing on the identification of all possible associations between all possible molecules and all possible targets. Thus, using chemogenomics approaches, one can obtain a biological profile of a molecule and even anticipate possible side effects.This thesis was focused on the development of approaches that aim to predict the binding of molecules to targets. In our lab, we focus on profiling molecular databases in order to get their full biological profile. Thus, my main work was related to this context and I tried to develop predictive models to assess the binding of ligands to proteins, to validate some virtual screening methods for profiling purpose, and finally, I developed an automatic hybrid profiling workflow that selects the best fitted virtual screening approach to use according the ligand/target context
Meslamani, Jamel Eddine. „Développement de nouvelles méthodes de criblage in silico en chémogénomique“. Phd thesis, Université de Strasbourg, 2012. http://tel.archives-ouvertes.fr/tel-00763448.
Der volle Inhalt der QuelleRocha, Jos? Luiz Carneiro da. „Caracteriza??o qu?mica e atividades biol?gicas in vitro e in silico de Asemeia ovata (Polygalaceae)“. Universidade Estadual de Feira de Santana, 2016. http://localhost:8080/tede/handle/tede/428.
Der volle Inhalt der QuelleMade available in DSpace on 2017-01-11T21:46:06Z (GMT). No. of bitstreams: 1 Boneco 97-2003-corre??es.pdf: 20164603 bytes, checksum: 78fbb46841fee330fc6bc340e1af3756 (MD5) Previous issue date: 2016-08-26
Funda??o de Amparo ? Pesquisa do Estado da Bahia - FAPEB
Polygalaceae family species are traditionally used in many regions of the world and because of this, research is being conducted to evaluate the biological activities, as well as phytochemicals aspects of these plants. In this way, the present study was to carry out the proposed chemical characterization and evaluation of biological activity in vitro of the extract and prediction of new biological activities in silico of the substances identified in Asemeia ovata (Polyagalaceae). The chemical characterization was made through previous phytochemical screening tests and fingerprint by HPLC-DAD. The isolation and identification of compounds was performed by classical chromatography techniques, HPLC-DAD and 1H and 13C NMR. The evaluation of the antioxidant activity in vitro was taken by Scavenging of DPPH free radical method, acetylcholinesterase activity by adapting the method of Ellman and Artemia salina lethality. The prediction of activity was made by tools for in silico target fishing, followed by docking the DOCK 6.7 program and evaluation of interaction profiles by Protein-Ligand Interaction server profiler. The chemical characterization showed that the extracts are rich in flavonoids and phenolic acids. It was possible to identify and quantify using HPLC-DAD substances: rutin, luteolin-7-O-glucoside, caffeic acid, p-coumaric acid and trans-ferulic acid. Moreover, it was possible to isolate the rutin substance, poligalen and a possible new alkaloid. The ethyl acetate extract was superior in the evaluation of in vitro activity with EC50 = 5.46 mg/mL for antioxidant activity, and LC50 = 71.91 mg/mL A. salina lethality. Acetylcholinesterase activity did not yield significant results (AChEIs% <20%). Tools for in silico target fishing allowed, through the ChemProt 2.0 and DRAR- CPI-servers, to select the molecular targets carbonic anhydrase 12 and epidermal growth factor receptor for routine; for luteolin-7-O-glucoside targets cotransporter 2 sodium / glucose and CDC42-activated protein kinase 1; poligalen to the target protein tyrosine kinase JAK2; and for caffeic acid, p-coumaric acid and trans-ferulic the best targets were epidermal growth factor receptor and Ras-related C3 botulinum toxin substrate 1, carbonic anhydrase 12 and Ornithine carbamoyltransferase, mitochondrial. This work provides new results for the species, both from a chemical and biological point of view, there is good prospects of study with interesting potential to be discovered.
Esp?cies da fam?lia Polygalaceae s?o utilizadas tradicionalmente em muitas regi?es do mundo e, devido a isso, pesquisas est?o sendo realizadas para avaliar as atividades biol?gicas, como tamb?m os aspectos fitoqu?micos desses vegetais. Desta forma, o presente trabalho teve como proposta realizar a caracteriza??o qu?mica e avalia??o de atividades biol?gicas in vitro de extratos da planta inteira e predi??o in silico de novas atividades biol?gicas das subst?ncias identificadas de Asemeia ovata (Polyagalaceae). A caracteriza??o qu?mica foi feita atrav?s de testes de triagem fitoqu?mica pr?via e fingerprint por CLAE-DAD. O isolamento e identifica??o de subst?ncias foi realizado por t?cnicas de cromatografia cl?ssica, CLAE-DAD e RMN de 1H e 13C. A avalia??o da atividade antioxidante in vitro foi feita pelo m?todo de sequestro de radical livre DPPH, atividade anticolinester?sica pela adapta??o do m?todo de Ellman e letalidade frente Artemia salina. A predi??o de atividades in silico foi feita por m?todos de Triagem Virtual Inversa (TVI), seguido de reacoplamento pelo programa DOCK 6.7 e avalia??o dos perfis de intera??o pelo servidor Protein-Ligand Interaction Profiler. A caracteriza??o qu?mica mostrou que os extratos s?o ricos em ?cidos fen?licos e flavonoides. Foi poss?vel identificar e quantificar, atrav?s de CLAE-DAD, as subst?ncias: rutina, luteolina-7-O-glicos?deo, ?cido cafeico, ?cido p-cum?rico e ?cido trans-fer?lico. Al?m disso, foi poss?vel isolar as subst?ncias rutina, poligaleno e um poss?vel novo alcaloide. O extrato acetato de etila mostrou-se superior na avali??o das atividades in vitro, com CE50 = 5,46 mg/mL para atividade antioxidante, e CL50 = 71,91 ?g/mL para letalidade frente a A. salina. Para a atividade anticolinester?sica n?o obteve-se resultados significativos (%IAChE < 20%). A TVI permitiu selecionar, atrav?s dos servidores ChemProt 2.0 e DRAR-CPI, os alvos moleculares Anidrase carb?nica 12 e Receptor de fator de crescimento epid?rmico para a rutina; para a luteolina-7-O-glicos?deo os alvos Cotransportador 2 de s?dio/glicose e Prote?na quinase CDC42 ativada 1; para o poligaleno o alvo Prote?na tirosina quinase JAK2; e para os ?cidos cafeico, p-cum?rico e trans-fer?lico os melhores alvos foram Receptor de fator de crescimento epid?rmico e Ras-relacionada ao substrato C3 da Toxina botul?nica 1, Anidrase carb?nica 12 e Ornitina carbamoiltransferase, mitocondrial. Esse trabalho fornece resultados in?ditos para a esp?cie, tanto do ponto de vista qu?mico, como biol?gico, apresentando boas perspectivas de estudo, com interessante potencial a ser descoberto.
Buchteile zum Thema "Docking inverse"
Ma, Zhiwei, und Xiaoqin Zou. „MDock: A Suite for Molecular Inverse Docking and Target Prediction“. In Methods in Molecular Biology, 313–22. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1209-5_18.
Der volle Inhalt der QuelleKumar, Ashwani, Ruchika Goyal und Sandeep Jain. „Docking Methodologies and Recent Advances“. In Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery, 295–319. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0115-2.ch012.
Der volle Inhalt der QuelleKumar, Ashwani, Ruchika Goyal und Sandeep Jain. „Docking Methodologies and Recent Advances“. In Oncology, 804–28. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-0549-5.ch031.
Der volle Inhalt der QuelleSaenz-Méndez, Patricia. „Multi-Target Drugs as Master Keys to Complex Diseases: Inverse Docking Strategies and Opportunities“. In Molecular Docking for Computer-Aided Drug Design, 295–311. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-12-822312-3.00005-9.
Der volle Inhalt der QuelleSantos Nascimento, Igor José dos, und Ricardo Olimpio de Moura. „Ligand and Structure-Based Drug Design (LBDD and SBDD): Promising Approaches to Discover New Drugs“. In Applied Computer-Aided Drug Design: Models and Methods, 1–32. BENTHAM SCIENCE PUBLISHERS, 2023. http://dx.doi.org/10.2174/9789815179934123010003.
Der volle Inhalt der QuelleHarms, Tekla A., und Julia A. Baldwin. „Paleoproterozoic geology of SW Montana: Implications for the paleogeography of the Wyoming craton and for the consolidation of Laurentia“. In Laurentia: Turning Points in the Evolution of a Continent. Geological Society of America, 2022. http://dx.doi.org/10.1130/2022.1220(05).
Der volle Inhalt der QuelleKonferenzberichte zum Thema "Docking inverse"
Alargić, Aleksa P., Bojan D. Levovnik und Miloš M. Svirčev. „Workflow automation of high-throughput inverse docking using Pharmmapper“. In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.678a.
Der volle Inhalt der QuelleVasseur, Romain, Stéphanie Baud, Luiz Angelo Steffenel, Xavier Vigouroux, Laurent Martiny, Michaël Krajecki und Manuel Dauchez. „Parallel strategies for an inverse docking method“. In the 20th European MPI Users' Group Meeting. New York, New York, USA: ACM Press, 2013. http://dx.doi.org/10.1145/2488551.2488584.
Der volle Inhalt der QuelleVentura, Jacopo, Marco Ciarcia, Marcello Romano und Ulrich Walter. „An Inverse Dynamics-Based Trajectory Planner for Autonomous Docking to a Tumbling Target“. In AIAA Guidance, Navigation, and Control Conference. Reston, Virginia: American Institute of Aeronautics and Astronautics, 2016. http://dx.doi.org/10.2514/6.2016-0876.
Der volle Inhalt der QuelleKim, Jin Seob, und Gregory S. Chirikjian. „Principles of Transference in Theoretical Kinematics“. In ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/detc2015-47624.
Der volle Inhalt der QuelleDe Silva, Sudam Chamikara, und Maroay Phlernjai. „Development and Evaluation of Inverted Docking Station for Small Quadrotor UAV“. In 2023 IEEE International Conference on Mechatronics and Automation (ICMA). IEEE, 2023. http://dx.doi.org/10.1109/icma57826.2023.10215697.
Der volle Inhalt der QuelleLeonard, Jeremie, Samer Aldhaher, Al Savvaris und Antonios Tsourdos. „Automated Recharging Station for Swarm of Unmanned Aerial Vehicles“. In ASME 2012 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/imece2012-88246.
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