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Статті в журналах з теми "Docking inverse":
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Darme, Pierre, Manuel Dauchez, Arnaud Renard, Laurence Voutquenne-Nazabadioko, Dominique Aubert, Sandie Escotte-Binet, Jean-Hugues Renault, Isabelle Villena, Luiz-Angelo Steffenel, and 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, no. 14 (July 13, 2021): 7489. http://dx.doi.org/10.3390/ijms22147489.
Анотація:
Molecular docking is widely used in computed drug discovery and biological target identification, but getting fast results can be tedious and often requires supercomputing solutions. AMIDE stands for AutoMated Inverse Docking Engine. It was initially developed in 2014 to perform inverse docking on High Performance Computing. AMIDE version 2 brings substantial speed-up improvement by using AutoDock-GPU and by pulling a total revision of programming workflow, leading to better performances, easier use, bug corrections, parallelization improvements and PC/HPC compatibility. In addition to inverse docking, AMIDE is now an optimized tool capable of high throughput inverse screening. For instance, AMIDE version 2 allows acceleration of the docking up to 12.4 times for 100 runs of AutoDock compared to version 1, without significant changes in docking poses. The reverse docking of a ligand on 87 proteins takes only 23 min on 1 GPU (Graphics Processing Unit), while version 1 required 300 cores to reach the same execution time. Moreover, we have shown an exponential acceleration of the computation time as a function of the number of GPUs used, allowing a significant reduction of the duration of the inverse docking process on large datasets.
2
Kammer, Daniel C., and Adam D. Steltzner. "Structural Identification of Mir Using Inverse System Dynamics and Mir/Shuttle Docking Data." Journal of Vibration and Acoustics 123, no. 2 (December 1, 2000): 230–37. http://dx.doi.org/10.1115/1.1355030.
Анотація:
The objective of this work was to investigate the use of inverse system identification techniques on Mir/Shuttle docking data to identify Mir vibrational characteristics for ultimate application to damage detection. A time-domain technique called a Remote Sensing System was proposed as an approach. The method uses inverse structural dynamics to identify vibrational characteristics of a structure. The Remote Sensing System method was demonstrated with a numerical simulation of Mir/Shuttle docking assuming that sensors were collocated with the Mir docking location. The method was then applied to the combined set of docking data from Mir/Shuttle missions STS-81, STS-89, and STS-91. Overall, the results produced by this work appear to indicate that Mir was in an undamaged state, at least with respect to docking excitation, at the time of STS-91. The significance of the contribution of the Remote Sensing System approach is that it is not affected by the nonstationarity and nonlinearity associated with the Mir/Shuttle docking interface, and docking forces at the interface do not have to be measured.
3
Kim, Stephanie S., Melanie L. Aprahamian, and Steffen Lindert. "Improving inverse docking target identification with Z ‐score selection." Chemical Biology & Drug Design 93, no. 6 (January 2, 2019): 1105–16. http://dx.doi.org/10.1111/cbdd.13453.
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Perez, German, Marcello Mascini, Valentina Lanzone, Manuel Sergi, Michele Del Carlo, Mauro Esposito, and 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.
Анотація:
A rapid and cost-effective computational methodology for designing and rationalizing the selection of small peptides as receptors for dioxin-like compounds was proposed. The backbone of the dioxin Ah receptor binding site was used to design a series of penta- and hexapeptide libraries, with 1400 elements in total. Peptide flexibility was considered and 10 conformers were found to be a good option to represent peptide conformational space with fair speed-accuracy ratio. Each peptide conformer was treated as a possible receptor, generating a dedicated box and then running a docking process using as ligands a family of 76 dibenzo-p-dioxins and 113 dibenzofurans mono- and polychlorinated. Significant predictions were confirmed by comparing primary structure of top and bottom ranked peptides binding dioxins confirming that scrambled positions of the same amino acids gave completely different predicted binding. The hexapeptide EWFQPW, with the best binding score, was chosen as selective sorbent material in solid-phase extraction. The retention performances were tested using the 2,3,7,8-tetrachlorodibenzo-p-dioxin and two polychlorinated biphenyls in order to verify the hexapeptide specificity. The solid-phase extraction experimental procedure was optimized, and analytical parameters of hexapeptide sorbent material were compared with the resin without hexapeptide and a commercial reversed phase cartridge.
5
Ma, Zhiwei, Xianjin Xu, and Xiaoqin Zou. "MDockServer: An Efficient Docking Platform for Inverse Virtual Screening." Biophysical Journal 114, no. 3 (February 2018): 56a. http://dx.doi.org/10.1016/j.bpj.2017.11.358.
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Xu, Xianjin, Marshal Huang, and Xiaoqin Zou. "Docking-based inverse virtual screening: methods, applications, and challenges." Biophysics Reports 4, no. 1 (February 2018): 1–16. http://dx.doi.org/10.1007/s41048-017-0045-8.
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Russo, Silvana, and Walter Filgueira De Azevedo. "Advances in the Understanding of the Cannabinoid Receptor 1 – Focusing on the Inverse Agonists Interactions." Current Medicinal Chemistry 26, no. 10 (June 20, 2019): 1908–19. http://dx.doi.org/10.2174/0929867325666180417165247.
Анотація:
Background: Cannabinoid Receptor 1 (CB1) is a membrane protein prevalent in the central nervous system, whose crystallographic structure has recently been solved. Studies will be needed to investigate CB1 complexes with its ligands and its role in the development of new drugs. Objective: Our goal here is to review the studies on CB1, starting with general aspects and focusing on the recent structural studies, with emphasis on the inverse agonists bound structures. Methods: We start with a literature review, and then we describe recent studies on CB 1 crystallographic structure and docking simulations. We use this structural information to depict protein-ligand interactions. We also describe the molecular docking method to obtain complex structures of CB 1 with inverse agonists. Results: Analysis of the crystallographic structure and docking results revealed the residues responsible for the specificity of the inverse agonists for CB 1. Most of the intermolecular interactions involve hydrophobic residues, with the participation of the residues Phe 170 and Leu 359 in all complex structures investigated in the present study. For the complexes with otenabant and taranabant, we observed intermolecular hydrogen bonds involving residues His 178 (otenabant) and Thr 197 and Ser 383 (taranabant). Conclusion: Analysis of the structures involving inverse agonists and CB 1 revealed the pivotal role played by residues Phe 170 and Leu 359 in their interactions and the strong intermolecular hydrogen bonds highlighting the importance of the exploration of intermolecular interactions in the development of novel inverse agonists.
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Kamal, Ahmed A. M., Lucia Petrera, Jens Eberhard, and Rolf W. Hartmann. "Structure–functionality relationship and pharmacological profiles of Pseudomonas aeruginosa alkylquinolone quorum sensing modulators." Organic & Biomolecular Chemistry 15, no. 21 (2017): 4620–30. http://dx.doi.org/10.1039/c7ob00263g.
Анотація:
Alkylquinolone derived compounds revealed four pharmacological profiles for PqsR modulation. Molecular docking illuminated the structural requirements. Only inverse agonists were effective pathoblockers inhibiting pyocyanin.
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Kämper, Andreas, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, and 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, no. 2 (March 2006): 903–11. http://dx.doi.org/10.1021/ci050467z.
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Ban, Tomohiro, Masahito Ohue, and 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.
Дисертації з теми "Docking inverse":
1
Vasseur, Romain. "Développements HPC pour une nouvelle méthode de docking inverse : applications aux protéines matricielles." Thesis, Reims, 2015. http://www.theses.fr/2015REIMS036.
Анотація:
Ce travail de thèse consiste au développement méthodologique et logiciel d'une méthode de docking moléculaire dite inverse. Cette méthode propose à travers le programme AMIDE — Automatic Inverse Docking Engine — de distribuer un grand nombres de simulations d'amarrage moléculaire sur des architectures HPC (clusters de calcul) avec les applications AutoDock 4.2 et AutoDock Vina. Le principe de cette méthode consiste à tester de petites molécules sur un ensemble de protéines cibles potentielles. Les paramètres optimaux ont été définis à partir d'une étude pilote et le protocole a été validé sur des ligands et peptides liants les protéines MMPs et EBP de la matrice extracellulaire. Cette méthode montre qu'elle permet d‘améliorer la recherche conformationnelle lors du calcul de docking sur des structures expérimentales par rapport à des protocoles existants (blind docking). Il est montré que le programme AMIDE permet de discriminer des sites de fixation privilégiés lors d'expériences de criblage inverse de protéines de manière plus performante que par blind docking. Ces résultats sont obtenus par la mise en place de méthodes de partitionnement de l'espace de recherche qui permettent également à travers un système de distribution hybride de déployer un ensemble de tâches indépendantes pour un traitement autorisant le passage d'échelleThis 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
2
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.
Анотація:
Les écorces d’arbres, co-produit de la sylviculture, constituent une source abondante et durable de substances naturelles. Toxoplasma gondii est le parasite responsable de la toxoplasmose, présentant une menace chez les fœtus, les nouveau-nés et les personnes immunodéprimées. Les thérapies actuelles, limitées et mal tolérées, font désormais face à des phénomènes de chimiorésistance. Ce travail de thèse a pour but d’explorer l’espace chimique associé aux écorces d’essences champardennaises, et les cibles protéiques essentielles à T. gondii. Une première évaluation in silico par docking inverse (AMIDEv2.0) a été réalisée afin d’identifier la cible biologique de triterpènes dérivés de la bétulone, isolés de l’Aulne glutineux ayant montré une activité anti-toxoplasmose in vitro. La CDPK3 a été identifiée comme étant la cible la plus probable parmi 87 protéines de T. gondii. Puis, une protéothèque de 25 structures protéiques 3D essentielles à la survie du parasite, 19 ayant été modélisées par homologie, a été constituée. Les composés de la Chimiothèque Nationale Essentielle ont été évalués ensuite sur cette protéothèque en utilisant AMIDEv2.0. Deux protéines ont été identifiées comme de potentielles cibles, dont ATG3, une structure reconstruite à partir d'homologues avec un pourcentage d'identité inférieur à 50%. Deuxièmement, les écorces du Mélèze d'Europe, dont l’extrait n-heptane avait démontré une activité significative (58 % d’inhibition de croissance parasitaire à 100 µg/ml), ont été soumises à un profilage chimique impliquant un fractionnement par Chromatographie de Partage Centrifuge et de déréplication combinant les données issues de la résonance magnétique nucléaire et de la spectrométrie de masse. Les outils VersaDB et CATHEDRAL ont été développés pour faciliter la création de bases de données modulables et l’évaluation du niveau de confiance des annotations. 52 molécules ont ainsi pu être annotées et associées à un score de confiance. En parallèle, des tests in vitro ont démontré que 2 des 12 fractions CPC, majoritairement composées de terpènes, inhibaient à plus de 40% la survie du parasite à 25 µg/ml. Les composés annotés chez L. decidua ont été soumis à AMIDEv2.0. Le croisement des résultats in vitro et in silico, reposant sur le calcul d'un score d'activité biologique, a mis en évidence l'acide 7-oxo-déhydroabiétique et l'acide daniellique, fortement corrélés à l'activité inhibitrice in vitro des écorces. La CDPK1 et la protéine SET containing Protein ont été identifiées comme leurs cibles protéiques probables, fournissant ainsi de premières informations sur leurs mécanismes d'action. Ces deux hits font actuellement l’objet d’une évaluation in vitro afin d’attester l’efficacité de la démarche développée au cours de ces travaux de thèseTree 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
3
Meslamani, Jamel-Eddine. "Développement de nouvelles méthodes de criblage in silico en chémogénomique." Thesis, Strasbourg, 2012. http://www.theses.fr/2012STRAF009/document.
Анотація:
La chémoinformatique et la bioinformatique sont des disciplines devenues indispensables à la découverte de médicaments. De nos jours, les industries pharmaceutiques consacrent près de 10% de leur budget de recherche et développement, à la recherche de médicaments assisté par ordinateur (Kapetanovic 2008). Cette émergence peut s’expliquer à la fois par le développement des architectures de calculs mais aussi par le faible coup qu’engendrent des analyses in silico par rapport à des tests in-vitro.Les essais biologiques qui ont été menés depuis des décennies afin d’identifier des médicaments potentiels, commencent à former une source très importante de données et plusieurs bases de données commencent à les répertorier. La disponibilité de ce type de données a favorisé le développement d’un nouvel axe de recherche appelé la "chémogénomique" et qui s’intéresse à l’étude et à l’identification des associations possibles entre plusieurs molécules et plusieurs cibles. Ainsi, la chémogénomique permet de déterminer le profil biologique d’une molécule et nous renseigne sur sa capacité à devenir une touche intéressante mais aussi à identifier ses possibles effets indésirables. Des méthodes de chémoinformatique permettent d’utiliser ces sources de données à des fins d’apprentissage et établir des modèles prédictifs qui permettront par la suite de faire des prédictions pour connaitre l’activité d’une molécule.Cette thèse a porté sur le développement et l'utilisation de méthodes de prédictions d’association protéine-ligand. La prédiction d’une association est importante en vue d’un criblage virtuel et peut s’effectuer à l’aide de plusieurs méthodes. Au sein du laboratoire, on s’intéresse plus particulièrement au profilage de bases de données de molécules (chimiothèques) contre une série de cibles afin d’établir leur profil biologique. J’ai donc essayé au cours de ma thèse de mettre au point des modèles prédictifs d’association protéine-ligand pour un grand nombre de cibles, valider des méthodes de criblage virtuel récentes à des fins de profilage mais aussi établir un protocole de profilage automatisé, qui décide du choix de la méthode de criblage la plus adaptée en s’appuyant sur les propriétés physico-chimiques du ligand à profiler et de l’éventuelle cibleChemoinformatics 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
4
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.
Анотація:
La chémoinformatique et la bioinformatique sont des disciplines devenues indispensables à la découverte de médicaments. De nos jours, les industries pharmaceutiques consacrent près de 10% de leur budget de recherche et développement, à la recherche de médicaments assisté par ordinateur (Kapetanovic 2008). Cette émergence peut s'expliquer à la fois par le développement des architectures de calculs mais aussi par le faible coup qu'engendrent des analyses in silico par rapport à des tests in-vitro.Les essais biologiques qui ont été menés depuis des décennies afin d'identifier des médicaments potentiels, commencent à former une source très importante de données et plusieurs bases de données commencent à les répertorier. La disponibilité de ce type de données a favorisé le développement d'un nouvel axe de recherche appelé la "chémogénomique" et qui s'intéresse à l'étude et à l'identification des associations possibles entre plusieurs molécules et plusieurs cibles. Ainsi, la chémogénomique permet de déterminer le profil biologique d'une molécule et nous renseigne sur sa capacité à devenir une touche intéressante mais aussi à identifier ses possibles effets indésirables. Des méthodes de chémoinformatique permettent d'utiliser ces sources de données à des fins d'apprentissage et établir des modèles prédictifs qui permettront par la suite de faire des prédictions pour connaitre l'activité d'une molécule.Cette thèse a porté sur le développement et l'utilisation de méthodes de prédictions d'association protéine-ligand. La prédiction d'une association est importante en vue d'un criblage virtuel et peut s'effectuer à l'aide de plusieurs méthodes. Au sein du laboratoire, on s'intéresse plus particulièrement au profilage de bases de données de molécules (chimiothèques) contre une série de cibles afin d'établir leur profil biologique. J'ai donc essayé au cours de ma thèse de mettre au point des modèles prédictifs d'association protéine-ligand pour un grand nombre de cibles, valider des méthodes de criblage virtuel récentes à des fins de profilage mais aussi établir un protocole de profilage automatisé, qui décide du choix de la méthode de criblage la plus adaptée en s'appuyant sur les propriétés physico-chimiques du ligand à profiler et de l'éventuelle cible.
5
Rocha, 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.
Анотація:
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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.
Частини книг з теми "Docking inverse":
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Ma, Zhiwei, and 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.
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Kumar, Ashwani, Ruchika Goyal, and 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.
Анотація:
Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
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Kumar, Ashwani, Ruchika Goyal, and 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.
Анотація:
Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
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Saenz-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.
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Santos Nascimento, Igor José dos, and 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.
Анотація:
The drug discovery and development process are challenging and have undergone many changes over the last few years. Academic researchers and pharmaceutical companies invest thousands of dollars a year to search for drugs capable of improving and increasing people's life quality. This is an expensive, time-consuming, and multifaceted process requiring the integration of several fields of knowledge. For many years, the search for new drugs was focused on Target-Based Drug Design methods, identifying natural compounds or through empirical synthesis. However, with the improvement of molecular modeling techniques and the growth of computer science, Computer-Aided Drug Design (CADD) emerges as a promising alternative. Since the 1970s, its main approaches, Structure-Based Drug Design (SBDD) and Ligand-Based Drug Design (LBDD), have been responsible for discovering and designing several revolutionary drugs and promising lead and hit compounds. Based on this information, it is clear that these methods are essential in drug design campaigns. Finally, this chapter will explore approaches used in drug design, from the past to the present, from classical methods such as bioisosterism, molecular simplification, and hybridization, to computational methods such as docking, molecular dynamics (MD) simulations, and virtual screenings, and how these methods have been vital to the identification and design of promising drugs or compounds. Finally, we hope that this chapter guides researchers worldwide in rational drug design methods in which readers will learn about approaches and choose the one that best fits their research.
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Harms, Tekla A., and 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).
Анотація:
ABSTRACT The Montana metasedimentary terrane (MMT) forms the NW margin of the Wyoming Province in present coordinates. The MMT preserves a multistage Paleoproterozoic tectonic history that clarifies the position of the Wyoming craton during assembly and breakup of the Precambrian Kenorland supercontinent and the subsequent assembly of Laurentia’s Precambrian basement. In SW Montana, burial, metamorphism, deformation, and partial melting attributed to orogeny were superimposed on Archean quartzofeldspathic orthogneisses and paragneisses at ca. 2.55 and ca. 2.45 Ga during the Tendoy and Beaverhead orogenies, respectively. Subsequent stability was disrupted at 2.06 Ga, when probable rift-related mafic dikes and sills intruded the older gneisses. The MMT was profoundly reworked by tectonism again as a consequence of the ca. 1.8–1.7 Ga Big Sky orogeny, during which juvenile metasupracrustal suites characteristic of an arc (the Little Belt arc) and back-arc basin collapsed against the Wyoming craton continental margin. The northern margin of the Wyoming craton occupied an upper-plate position south of a south-dipping subduction zone at that time. Lithostratigraphic correlations link the southeastern Wyoming and southern Superior cratons at ca. 2.45 Ga with the Wyoming craton joined to the Kenorland supercontinent in an inverted position relative to present coordinates. This places the MMT along an open supercontinental margin, in a position permissive of collision or accretion and orogeny during a time when other parts of Kenorland were experiencing mafic volcanism and incipient rifting. The ca. 2.45 Ga Beaverhead orogeny in the MMT was most likely the consequence of collision with one of the Rae family of cratons, which share a history of tectonism at this time. The Beaverhead collision enveloped the Wyoming craton in a larger continental landmass and led to the 2.45–2.06 Ga period of tectonic quiescence in the MMT. Breakup of Kenorland occurred ca. 2.2–2.0 Ga. In the MMT, this is expressed by the 2.06 Ga mafic dikes and sills that crosscut older gneisses. The Wyoming craton would have been an island continent within the Manikewan Ocean after rifting from Kenorland on one side and from the Rae family craton on the MMT side. Subduction beneath the MMT in the Wyoming craton started no later than 1.87 Ga and was active until 1.79 Ga. This opened a back-arc basin and created the Little Belt arc to the north of the craton, contributed to the demise of the Manikewan Ocean, and culminated in collision along the Big Sky orogen starting ca. 1.78 Ga. Collision across the Trans-Hudson orogen in Canada occurred during a slightly earlier period. Thus, docking of the Wyoming craton reflects the final stage in the closure of the Manikewan Ocean and the amalgamation of the Archean cratons of Laurentia.
Тези доповідей конференцій з теми "Docking inverse":
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Alargić, Aleksa P., Bojan D. Levovnik, and 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.
Анотація:
In this paper, we present a novel, modular script Pharmmapper-Mass-Docker for the inverse docking workflow automation based on the pharmacophore screening results obtained on the Pharmmapper server. Pharmmapper-Mass-Docker streamlines download, manipulation, and entire inverse docking of the Pharmmapper results, encompassing essential steps like ligand/gridbox/binding site coordinate extraction (via centroid generation) and obtaining the output data ready for further comprehensive data analysis. By automating the entire inverse docking procedure, our modular script potentially enhances data management efficiency during inverse docking and reverse screening, empowering the researchers to efficiently discover and explore novel protein-ligand interactions.
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Vasseur, Romain, Stéphanie Baud, Luiz Angelo Steffenel, Xavier Vigouroux, Laurent Martiny, Michaël Krajecki, and 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.
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Ventura, Jacopo, Marco Ciarcia, Marcello Romano, and 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.
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Kim, Jin Seob, and 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.
Анотація:
The concept of symmetrical parameterizations of rigid-body motions was introduced in a paper in the Yang Symposium in 2014 in the context of biomolecular docking applications. These parameters are symmetrical in the sense that they “look the same” in a motion and in its inverse. Here we examine properties of special symmetrical parameterizations of rotations and full rigid-body motions in the plane and three-dimensional space. In particular, it is shown how special kinds of motions can “pass through”, or transfer, from left to right. And conjugations of rotation or homogeneous transforms can transfer to the symmetrical parameters.
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De Silva, Sudam Chamikara, and 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.
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Leonard, Jeremie, Samer Aldhaher, Al Savvaris, and 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.
Анотація:
Automated maintenance has become a necessity for UAV systems to allow human operators to concentrate on higher-level tasks. By reducing the need for a human interaction, such systems could be set to function in remote environments for an extended period of time and take care of a higher number of vehicles. This paper describes the work carried out to design, test and construct an autonomous charging station for battery-powered quadrotors. In the effort to fit swarm behaviors, the focus has been to shorten the charging phase of a single quadrotor platform. By designing safer electrical contacts and adding a cell balancer to the system, the station can supply considerably more current to charge the vehicle’s battery. Once the vehicle has landed, voltage and current probes transmit the current state-of-charge to a controller for optimum charging cycle. To support even more applications, the system was equipped with the capability of wireless power transfer. Energy is transferred from a power transmitter in the docking station to a power receiver on-board the vehicle based on resonant inductive coupling. Minimizing the internal losses of the DC/AC inverter and AC/DC rectifier in the transmitter and receiver will allow for higher power levels to be transmitted and will maximize the efficiency. With the continuous monitoring of the process and the advanced charging technologies allowing for a balanced high-current charge, the Flying/Charging ratio of the vehicle could reach 1.