Littérature scientifique sur le sujet « Molecuar dynamics and docking simulation »
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Articles de revues sur le sujet "Molecuar dynamics and docking simulation"
Naqvi, Ahmad Abu Turab, Taj Mohammad, Gulam Mustafa Hasan et 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 (31 décembre 2018) : 1755–68. http://dx.doi.org/10.2174/1568026618666181025114157.
Texte intégral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.
Texte intégralMiyagawa, Hiroh, et 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.
Texte intégralMeng, Fancui. « Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds ». Journal of Theoretical Chemistry 2013 (4 décembre 2013) : 1–7. http://dx.doi.org/10.1155/2013/739574.
Texte intégralBathelt, Christine, Rolf Schmid et Jürgen Pleiss. « Regioselectivity of CYP2B6 : homology modeling, molecular dynamics simulation, docking ». Journal of Molecular Modeling 8, no 11 (1 novembre 2002) : 327–35. http://dx.doi.org/10.1007/s00894-002-0104-y.
Texte intégralKurniawan, Isman, Muhammad Salman Fareza et Ponco Iswanto. « CoMFA, Molecular Docking and Molecular Dynamics Studies on Cycloguanil Analogues as Potent Antimalarial Agents ». Indonesian Journal of Chemistry 21, no 1 (14 septembre 2020) : 66. http://dx.doi.org/10.22146/ijc.52388.
Texte intégralKhare, 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 (12 juin 2022) : 770. http://dx.doi.org/10.3390/brainsci12060770.
Texte intégralZaki, Magdi E. A., Sami A. Al-Hussain, Vijay H. Masand, Siddhartha Akasapu, Sumit O. Bajaj, Nahed N. E. El-Sayed, Arabinda Ghosh et 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 (13 avril 2021) : 357. http://dx.doi.org/10.3390/ph14040357.
Texte intégralDe Paris, Renata, Christian V. Quevedo, Duncan D. Ruiz, Osmar Norberto de Souza et 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.
Texte intégralLuo, Lianxiang, Ai Zhong, Qu Wang et 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 (25 décembre 2021) : 29. http://dx.doi.org/10.3390/md20010029.
Texte intégralThèses sur le sujet "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.
Texte intégralUllmann, 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.
Texte intégralMadhusudhan, 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.
Texte intégralSousa, 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.
Texte intégralInterleukin 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.
Texte intégralDrepanocytosis 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.
Texte intégralOne 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.
Texte intégralThe 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.
Texte intégralThis 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.
Texte intégralLundborg, 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.
Texte intégralAt 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.
Livres sur le sujet "Molecuar dynamics and docking simulation"
Zaheer Ul-Haq et Angela K. Wilson, dir. Frontiers in Computational Chemistry : Volume 6. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150368481220601.
Texte intégralChapitres de livres sur le sujet "Molecuar dynamics and docking simulation"
Sapay, Nicolas, Alessandra Nurisso et Anne Imberty. « Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water ». Dans Methods in Molecular Biology, 469–83. Totowa, NJ : Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_18.
Texte intégralRanimol, G., C. B. Devipriya et Swetha Sunkar. « Docking and Molecular Dynamics Simulation Studies for the Evaluation of Laccase Mediated Biodegradation of Triclosan ». Dans 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.
Texte intégralRodríguez, Maricarmen Hernández, Leticia Guadalupe Fragoso Morales, José Correa Basurto et Martha Cecilia Rosales Hernández. « Molecular Docking and Molecular Dynamics Simulation to Evaluate Compounds That Avoid the Amyloid Beta 1-42 Aggregation ». Dans Neuromethods, 229–48. New York, NY : Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7404-7_9.
Texte intégralSantos, Lucianna H. S., Rafaela S. Ferreira et Ernesto R. Caffarena. « Integrating Molecular Docking and Molecular Dynamics Simulations ». Dans 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.
Texte intégralKumar, A., E. Rathi et S. G. Kini. « Fragment-based Design of Novel Inhibitors of HPV 16 E6 Oncoprotein : Molecular Docking, Molecular Dynamics Simulation and In Silico ADME Analysis ». Dans Special Publications, 25–30. Cambridge : Royal Society of Chemistry, 2019. http://dx.doi.org/10.1039/9781839160783-00025.
Texte intégralBekker, Gert-Jan, et Narutoshi Kamiya. « Dynamic Docking Using Multicanonical Molecular Dynamics : Simulating Complex Formation at the Atomistic Level ». Dans Methods in Molecular Biology, 187–202. New York, NY : Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1209-5_11.
Texte intégralSingh, Sakshi, Qanita Bani Baker et Dev Bukhsh Singh. « Molecular docking and molecular dynamics simulation ». Dans Bioinformatics, 291–304. Elsevier, 2022. http://dx.doi.org/10.1016/b978-0-323-89775-4.00014-6.
Texte intégralPriya, Prerna, Minu Kesheri, Rajeshwar P. Sinha et Swarna Kanchan. « Molecular Dynamics Simulations for Biological Systems ». Dans Pharmaceutical Sciences, 1044–71. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-1762-7.ch040.
Texte intégralPriya, Prerna, Minu Kesheri, Rajeshwar P. Sinha et Swarna Kanchan. « Molecular Dynamics Simulations for Biological Systems ». Dans Advances in Bioinformatics and Biomedical Engineering, 286–313. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-4666-8811-7.ch014.
Texte intégralAnthony, Josephine, Vijaya Raghavan Rangamaran, Kumar T. Shivasankarasubbiah, Dharani Gopal et Kirubagaran Ramalingam. « Applications of Molecular Docking ». Dans Advances in Medical Technologies and Clinical Practice, 278–306. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0362-0.ch011.
Texte intégralActes de conférences sur le sujet "Molecuar dynamics and docking simulation"
Arba, Muhammad, Rahmana Emran Kartasasmita et Daryono H. Tjahjono. « Molecular Docking and Molecular Dynamics Simulation of the Interaction of Cationic Imidazolium Porphyrin-Anthraquinone and Hsp90 ». Dans 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.
Texte intégralRahmatia, Fahmi, Tony Sumaryada, Setyanto Tri Wahyudi et Hendradi Hardhienata. « Docking effects of curcuminoid ligands on protein L stability using molecular dynamics simulation with temperature variations ». Dans INTERNATIONAL CONFERENCE ON SCIENCE AND APPLIED SCIENCE (ICSAS) 2021. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0073790.
Texte intégralKandt, Christian, Eliud O. Oloo et D. Peter Tieleman. « Domain coupling in the ABC transporter system BtuCD/BtuF : molecular dynamics simulation, normal mode analysis and protein-protein docking ». Dans 21st International Symposium on High Performance Computing Systems and Applications (HPCS'07). IEEE, 2007. http://dx.doi.org/10.1109/hpcs.2007.15.
Texte intégralJovanović-Šanta, Suzana S., Esma Isenović, Julijana A. Petrović et Yaraslau U. Dzichenka. « BINDING OF 17-SUBSTITUTED 16-NITRILE 16,17-SECOESTRANE COMPOUNDS TO ESTROGEN RECEPTORS – „IN VITRO“ AND „IN SILICO“ STUDY ». Dans 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.403js.
Texte intégralAlvarado-Huayhuaz, Jesus Antonio, Wilmar Puma-Zamora et Ana Cecilia Valderrama-Negrón. « In-silico study of antituberculous activity of Zn-pyrazinamide in pyrazinamidase ». Dans VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020-89.
Texte intégralGhofranian, Siamak, Matthew Schmidt, John Schliesing, Tim Briscoe et John McManamen. « Simulation of Shuttle/Mir docking ». Dans 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.
Texte intégralDimić, Dušan, Dejan Milenković, Edina Avdović, Goran Kaluđerović et Jasmina Dimitrić Marković. « MOLECULAR DOCKING AND MOLECULAR DYNAMICS STUDIES OF THE INTERACTION BETWEEN COUMARIN-NEUROTRANSMITTER DERIVATIVES AND CARBONIC ANHYDRASE IX ». Dans 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.056d.
Texte intégralProbe, Austin, et John L. Junkins. « Robotic Simulation Experiments Demonstrating Docking Proximity Operations and Contact Dynamics ». Dans AIAA Modeling and Simulation Technologies Conference. Reston, Virginia : American Institute of Aeronautics and Astronautics, 2014. http://dx.doi.org/10.2514/6.2014-1493.
Texte intégralKrenek, Ales, Martin Petrek, Jan Kmunicek, Jiri Filipovic, Zdenek Sustr, Frantisek Dvorak, Jiri Sitera, Jiri Wiesner et Ludek Matyska. « Multiple Ligand Trajectory Docking Study - Semiautomatic Analysis of Molecular Dynamics Simulations using EGEE gLite Services ». Dans 16th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP 2008). IEEE, 2008. http://dx.doi.org/10.1109/pdp.2008.71.
Texte intégralShi, Keke, Zhaowei Sun, Chuang Liu et Dong Ye. « Dynamics modeling and simulation of space electromagnetic docking for CubeSat ». Dans 2017 8th International Conference on Mechanical and Aerospace Engineering (ICMAE). IEEE, 2017. http://dx.doi.org/10.1109/icmae.2017.8038716.
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