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Статті в журналах з теми "Molecuar dynamics and docking simulation"
Naqvi, Ahmad Abu Turab, Taj Mohammad, Gulam Mustafa Hasan, and Md Imtaiyaz Hassan. "Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships." Current Topics in Medicinal Chemistry 18, no. 20 (December 31, 2018): 1755–68. http://dx.doi.org/10.2174/1568026618666181025114157.
Повний текст джерела李, 博. "Progress in Molecular Docking and Molecular Dynamics Simulation." Journal of Comparative Chemistry 03, no. 01 (2019): 1–10. http://dx.doi.org/10.12677/cc.2019.31001.
Повний текст джерелаMiyagawa, Hiroh, and Kunihiro Kitamura. "1P565 Molecular dynamics simulations of association and docking between an inhibitor and an enzyme.(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S288. http://dx.doi.org/10.2142/biophys.46.s288_1.
Повний текст джерелаMeng, Fancui. "Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds." Journal of Theoretical Chemistry 2013 (December 4, 2013): 1–7. http://dx.doi.org/10.1155/2013/739574.
Повний текст джерелаBathelt, Christine, Rolf Schmid, and Jürgen Pleiss. "Regioselectivity of CYP2B6: homology modeling, molecular dynamics simulation, docking." Journal of Molecular Modeling 8, no. 11 (November 1, 2002): 327–35. http://dx.doi.org/10.1007/s00894-002-0104-y.
Повний текст джерелаKurniawan, Isman, Muhammad Salman Fareza, and Ponco Iswanto. "CoMFA, Molecular Docking and Molecular Dynamics Studies on Cycloguanil Analogues as Potent Antimalarial Agents." Indonesian Journal of Chemistry 21, no. 1 (September 14, 2020): 66. http://dx.doi.org/10.22146/ijc.52388.
Повний текст джерелаKhare, Noopur, Sanjiv Kumar Maheshwari, Syed Mohd Danish Rizvi, Hind Muteb Albadrani, Suliman A. Alsagaby, Wael Alturaiki, Danish Iqbal, et al. "Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer’s Disease." Brain Sciences 12, no. 6 (June 12, 2022): 770. http://dx.doi.org/10.3390/brainsci12060770.
Повний текст джерелаZaki, Magdi E. A., Sami A. Al-Hussain, Vijay H. Masand, Siddhartha Akasapu, Sumit O. Bajaj, Nahed N. E. El-Sayed, Arabinda Ghosh, and Israa Lewaa. "Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis." Pharmaceuticals 14, no. 4 (April 13, 2021): 357. http://dx.doi.org/10.3390/ph14040357.
Повний текст джерелаDe Paris, Renata, Christian V. Quevedo, Duncan D. Ruiz, Osmar Norberto de Souza, and Rodrigo C. Barros. "Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments." Computational Intelligence and Neuroscience 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/916240.
Повний текст джерелаLuo, Lianxiang, Ai Zhong, Qu Wang, and Tongyu Zheng. "Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, ADMET, and Molecular Dynamics (MD) Simulation of Potential Inhibitors of PD-L1 from the Library of Marine Natural Products." Marine Drugs 20, no. 1 (December 25, 2021): 29. http://dx.doi.org/10.3390/md20010029.
Повний текст джерелаДисертації з теми "Molecuar dynamics and docking simulation"
Trezza, Alfonso. "A novel computational way to unlock drug targets deep and transient secretes." Doctoral thesis, Università di Siena, 2019. http://hdl.handle.net/11365/1072788.
Повний текст джерелаUllmann, 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.
Повний текст джерелаMadhusudhan, M. S. "Computer Modeling and Molecular Dynamics Simulation Of Angiogenins And Its Ligand Bound Complexes." Thesis, Indian Institute of Science, 2000. http://hdl.handle.net/2005/211.
Повний текст джерелаSousa, Rui. "Structural insights of Interleukin-15 through Molecular Dynamics simulations : Towards the rational design of specific inhibitors." Thesis, Nantes, 2019. http://www.theses.fr/2019NANT4081.
Повний текст джерелаInterleukin 15 (IL-15) is a cytokine involved in a plethora of different cellular functions. It participates, for instance, in the development and activation of immune responses. IL-15 has, therefore, clearly appeared as a potential target for several therapeutic applications. The structure of this cytokine is based on a quaternary complex between IL-15 and its a (IL-15Ra), b ( IL-2Rβ) and y (yc) receptors. The key to the functional modulation of IL-15 lies on its interaction with its receptors and, more particularly, with IL-2Rβ. Interleukin-2 sharing two out of the three receptors 2Rβ and yc), the search for specific IL-15 inhibitors has to take into account these features. In this work, through various Molecular Modeling approaches, specifically Molecular Dynamics (MD) simulations, we have (i) determined the influence of the complexed form of IL-15 (dimer, trimer or tetramer) on the interface properties (ii) highlighted the key amino acid (“hot spots”) of the various interfaces (iii) studied the impact of mutations of selected residues (iv) used this information to design a pharmacophore which has allowed, in a subsequent step, the discovery of new low-molecular weight compounds able to specifically target one of the IL-15 interfaces (IL- 15/ IL-2Rβ). The theoretical data have been compared to the results of biological experiments carried out in the framework of the project
Madeleine, Noelly. "Recherche d'inhibiteurs de l'interaction Lutheran-Laminine par des techniques de modélisation et de simulation moléculaires." Thesis, La Réunion, 2017. http://www.theses.fr/2017LARE0054/document.
Повний текст джерелаDrepanocytosis is a genetic blood disorder characterized by red blood cells that assume an abnormal sickle shape. In the pathogenesis of vaso-occlusive crises of sickle cell disease, red blood cells bind to the vascular endothelium and promote vaso-occlusion. At the surface of these sickle red blood cells, the overexpressed protein Lutheran (Lu) strongly interacts with the Laminin (Ln) 511/521.The aim of this study was to identify a protein-protein interaction (PPI) inhibitor with a highprobability of binding to Lu for the inhibition of the Lu-Ln 511/521 interaction. A virtual screening was performed with 1 295 678 compounds that target Lu. Prior validation of a robust scoring protocol was considered on the protein CD80 because this protein has a binding site with similar topological and physico-chemical characteristics and it also has a series of ligands with known affinity constants. This protocol consisted of multiple filtering steps based on calculated affinities (scores), molecular dynamics simulations and molecular properties. A robust scoring protocol was validated on the protein CD80 with the docking program DOCK6 and the scoring functions XSCORE and MM-PBSA and also with the FMO method. This protocol was applied to the protein Lu and we found two compounds that were validated by in vitro studies. The protection of these ligands by a patent is under process. Nine other compounds were identified by the scoring functionXSCORE and seem to be promising candidates for inhibiting the Lu-Ln 511/521 interaction
Haslak, Zeynep Pinar. "Approches numériques pour évaluer les propriétés de liaison de ligands : le cas du récepteur NMDA." Electronic Thesis or Diss., Université de Lorraine, 2019. http://www.theses.fr/2019LORR0240.
Повний текст джерелаOne of the important issues in drug design is the identification of the biological activity of receptor ligands. Development, synthesis and activity measurements of ligands have a major importance in drug design. However, there are certain limits in experimental studies; synthesis of a large number of compounds to cover all the potentially active molecules is unrealistic. Computational studies could therefore provide a valuable aid to experimental studies on ligand design for glutamate receptors. By combining the strengths of Molecular Dynamics and Quantum Chemical approaches, a more focused inspection, characterisation and rationalization of the drug design studies is allowed to be established. In this dissertation, computational methods have been used to investigate the intrinsic properties of the biologically active molecules that cause the selectivity. The results of this study will be introduced in 4 chapters. In Chapters 4 and 5, we aimed to differentiate between agonists, antagonists and partial agonists based on Quantum Chemical descriptors and binding Gibbs free energies. Several molecular properties that could play a role in ligand binding to the glycine GluN1 subunit of NMDA and calculated binding Gibbs free energies were further used to provide a link between the efficacies and binding affinities of the ligands. Prediction of the acid dissociation constants of amino acids in proteins and ligands allows us to have information about the binding affinity and efficacy of the ligand to its target protein. Considering the significance of p\textit{K_a}'s, how atomic charges of carboxylic acids can be related to the prediction of p\textit{K_a} of the ligands have been explored in Chapter 6. In order to shed light on the origins of the stereoselectivity of biologically active ligands, several mechanistic pathways have been evaluated for 2-thiohydantoins which are potent androgen receptor antagonists and the results are given in Chapter 7
Touzeau, Jérémy. "Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales." Thesis, Sorbonne Paris Cité, 2018. https://theses.md.univ-paris-diderot.fr/Touzeau_jeremy_2_complete_20181203.pdf.
Повний текст джерелаThe tailoring of devices involving biomolecules, for applications such as the detection (biosensors) or protection against pathogens (antimicrobial coats), still introduce several interrogations at an atomic point of view. In this context, we used molecular modelling tools in order to realize multi-scale studies (quantic level and molecular mechanics level) about experimental systems and solve issues. We interested in two projects. In the first one, we firstly focused on biosensor involving filed effect transistor (EGOFET type), by studying the optimization of the semi-conductor channel. Then we interested in the specific biological interaction of the biosensor. In the second one, we interested in an antimicrobial coat. This device is composed by a peptide containing three parts: an anchoring one, a cleavable one which can be cut specifically by a surface protease of the target and so, release the last peptide in the area which involves antimicrobial properties. The system is very efficient in solution but when it’s grafted on a surface, antimicrobial properties disappear. Consequently, we used molecular modelling tools in order to prospect those antimicrobial properties loss
Krebs, Fanny. "Etudes in silico et expérimentale de la DXR & synthèse de D- et L-GAP énantiomériquement purs." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAF059/document.
Повний текст джерелаThis thesis concerns the study of the 2 first enzymes of the MEP pathway: DXS and DXR. The MEP pathway permits the biosynthesis of isoprénoïdes in most bacteria, including pathogenic one. As it is not present in human, enzymes of MEP pathway are effective targets in the research of new antimicrobial drugs. The objective was to advance the development of new antimicrobiotic compounds. We used computational tools: molecular docking and molecular dynamics simulations coupled with an MM/PBSA approach. We were able to identify residues that contribute significantly to the ligand binding in the DXR active site. These results were used to guide the conception of new inhibitor models, such as bisubstrates, biligands and α,α-difluoro phosphonates, two of which were synthetized. We also developed a synthesis method to obtain L- and D-GAP as enantiomerically pure molecules. The goal was to study the enantiospecificity of DXS to its substrate, D-GAP
Abdulganiyyu, Ibrahim A. "A single AKH neuropeptide activating three different fly AKH-receptors: an insecticide study via computational methods." Doctoral thesis, Faculty of Science, 2021. http://hdl.handle.net/11427/33621.
Повний текст джерелаLundborg, Magnus. "Computer-Assisted Carbohydrate Structural Studies and Drug Discovery." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-56411.
Повний текст джерелаAt the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript. Paper 6. Manuscript.
Книги з теми "Molecuar dynamics and docking simulation"
Zaheer Ul-Haq and Angela K. Wilson, eds. Frontiers in Computational Chemistry: Volume 6. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150368481220601.
Повний текст джерелаЧастини книг з теми "Molecuar dynamics and docking simulation"
Sapay, Nicolas, Alessandra Nurisso, and Anne Imberty. "Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water." In Methods in Molecular Biology, 469–83. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_18.
Повний текст джерелаRanimol, G., C. B. Devipriya, and Swetha Sunkar. "Docking and Molecular Dynamics Simulation Studies for the Evaluation of Laccase Mediated Biodegradation of Triclosan." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 205–13. Dordrecht: Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_20.
Повний текст джерелаRodríguez, Maricarmen Hernández, Leticia Guadalupe Fragoso Morales, José Correa Basurto, and Martha Cecilia Rosales Hernández. "Molecular Docking and Molecular Dynamics Simulation to Evaluate Compounds That Avoid the Amyloid Beta 1-42 Aggregation." In Neuromethods, 229–48. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7404-7_9.
Повний текст джерелаSantos, Lucianna H. S., Rafaela S. Ferreira, and Ernesto R. Caffarena. "Integrating Molecular Docking and Molecular Dynamics Simulations." In Methods in Molecular Biology, 13–34. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9752-7_2.
Повний текст джерелаKumar, A., E. Rathi, and S. G. Kini. "Fragment-based Design of Novel Inhibitors of HPV 16 E6 Oncoprotein: Molecular Docking, Molecular Dynamics Simulation and In Silico ADME Analysis." In Special Publications, 25–30. Cambridge: Royal Society of Chemistry, 2019. http://dx.doi.org/10.1039/9781839160783-00025.
Повний текст джерелаBekker, Gert-Jan, and Narutoshi Kamiya. "Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level." In Methods in Molecular Biology, 187–202. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1209-5_11.
Повний текст джерелаSingh, Sakshi, Qanita Bani Baker, and Dev Bukhsh Singh. "Molecular docking and molecular dynamics simulation." In Bioinformatics, 291–304. Elsevier, 2022. http://dx.doi.org/10.1016/b978-0-323-89775-4.00014-6.
Повний текст джерелаPriya, Prerna, Minu Kesheri, Rajeshwar P. Sinha, and Swarna Kanchan. "Molecular Dynamics Simulations for Biological Systems." In Pharmaceutical Sciences, 1044–71. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-1762-7.ch040.
Повний текст джерелаPriya, Prerna, Minu Kesheri, Rajeshwar P. Sinha, and Swarna Kanchan. "Molecular Dynamics Simulations for Biological Systems." In Advances in Bioinformatics and Biomedical Engineering, 286–313. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-4666-8811-7.ch014.
Повний текст джерелаAnthony, Josephine, Vijaya Raghavan Rangamaran, Kumar T. Shivasankarasubbiah, Dharani Gopal, and Kirubagaran Ramalingam. "Applications of Molecular Docking." In Advances in Medical Technologies and Clinical Practice, 278–306. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0362-0.ch011.
Повний текст джерелаТези доповідей конференцій з теми "Molecuar dynamics and docking simulation"
Arba, Muhammad, Rahmana Emran Kartasasmita, and Daryono H. Tjahjono. "Molecular Docking and Molecular Dynamics Simulation of the Interaction of Cationic Imidazolium Porphyrin-Anthraquinone and Hsp90." In 3rd International Conference on Computation for Science and Technology (ICCST-3). Paris, France: Atlantis Press, 2015. http://dx.doi.org/10.2991/iccst-15.2015.1.
Повний текст джерелаRahmatia, Fahmi, Tony Sumaryada, Setyanto Tri Wahyudi, and Hendradi Hardhienata. "Docking effects of curcuminoid ligands on protein L stability using molecular dynamics simulation with temperature variations." In INTERNATIONAL CONFERENCE ON SCIENCE AND APPLIED SCIENCE (ICSAS) 2021. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0073790.
Повний текст джерелаKandt, Christian, Eliud O. Oloo, and D. Peter Tieleman. "Domain coupling in the ABC transporter system BtuCD/BtuF: molecular dynamics simulation, normal mode analysis and protein-protein docking." In 21st International Symposium on High Performance Computing Systems and Applications (HPCS'07). IEEE, 2007. http://dx.doi.org/10.1109/hpcs.2007.15.
Повний текст джерелаJovanović-Šanta, Suzana S., Esma Isenović, Julijana A. Petrović, and Yaraslau U. Dzichenka. "BINDING OF 17-SUBSTITUTED 16-NITRILE 16,17-SECOESTRANE COMPOUNDS TO ESTROGEN RECEPTORS – „IN VITRO“ AND „IN SILICO“ STUDY." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.403js.
Повний текст джерелаAlvarado-Huayhuaz, Jesus Antonio, Wilmar Puma-Zamora, and Ana Cecilia Valderrama-Negrón. "In-silico study of antituberculous activity of Zn-pyrazinamide in pyrazinamidase." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020-89.
Повний текст джерелаGhofranian, Siamak, Matthew Schmidt, John Schliesing, Tim Briscoe, and John McManamen. "Simulation of Shuttle/Mir docking." In 36th Structures, Structural Dynamics and Materials Conference. Reston, Virigina: American Institute of Aeronautics and Astronautics, 1995. http://dx.doi.org/10.2514/6.1995-1197.
Повний текст джерелаDimić, Dušan, Dejan Milenković, Edina Avdović, Goran Kaluđerović, and Jasmina Dimitrić Marković. "MOLECULAR DOCKING AND MOLECULAR DYNAMICS STUDIES OF THE INTERACTION BETWEEN COUMARIN-NEUROTRANSMITTER DERIVATIVES AND CARBONIC ANHYDRASE IX." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.056d.
Повний текст джерелаProbe, Austin, and John L. Junkins. "Robotic Simulation Experiments Demonstrating Docking Proximity Operations and Contact Dynamics." In AIAA Modeling and Simulation Technologies Conference. Reston, Virginia: American Institute of Aeronautics and Astronautics, 2014. http://dx.doi.org/10.2514/6.2014-1493.
Повний текст джерелаKrenek, Ales, Martin Petrek, Jan Kmunicek, Jiri Filipovic, Zdenek Sustr, Frantisek Dvorak, Jiri Sitera, Jiri Wiesner, and Ludek Matyska. "Multiple Ligand Trajectory Docking Study - Semiautomatic Analysis of Molecular Dynamics Simulations using EGEE gLite Services." In 16th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP 2008). IEEE, 2008. http://dx.doi.org/10.1109/pdp.2008.71.
Повний текст джерелаShi, Keke, Zhaowei Sun, Chuang Liu, and Dong Ye. "Dynamics modeling and simulation of space electromagnetic docking for CubeSat." In 2017 8th International Conference on Mechanical and Aerospace Engineering (ICMAE). IEEE, 2017. http://dx.doi.org/10.1109/icmae.2017.8038716.
Повний текст джерела