Добірка наукової літератури з теми "Standard Binding Free Energy"
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Статті в журналах з теми "Standard Binding Free Energy":
Kötter, Alex, Henning D. Mootz, and Andreas Heuer. "Standard Binding Free Energy of a SIM–SUMO Complex." Journal of Chemical Theory and Computation 15, no. 11 (September 17, 2019): 6403–10. http://dx.doi.org/10.1021/acs.jctc.9b00428.
General, Ignacio J. "A Note on the Standard State’s Binding Free Energy." Journal of Chemical Theory and Computation 6, no. 8 (July 15, 2010): 2520–24. http://dx.doi.org/10.1021/ct100255z.
Zhang, Hong, Hugo Gattuso, Elise Dumont, Wensheng Cai, Antonio Monari, Christophe Chipot, and François Dehez. "Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA." Molecules 23, no. 2 (January 25, 2018): 228. http://dx.doi.org/10.3390/molecules23020228.
Doudou, Slimane, Neil A. Burton, and Richard H. Henchman. "Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force." Journal of Chemical Theory and Computation 5, no. 4 (March 10, 2009): 909–18. http://dx.doi.org/10.1021/ct8002354.
Jandova, Zuzana, Willem Jespers, Eddy Sotelo, Hugo Gutiérrez-de-Terán, and Chris Oostenbrink. "Free-Energy Calculations for Bioisosteric Modifications of A3 Adenosine Receptor Antagonists." International Journal of Molecular Sciences 20, no. 14 (July 16, 2019): 3499. http://dx.doi.org/10.3390/ijms20143499.
Lanez, Touhami, and Meriem Henni. "Spectrophotometrical study of antioxidant standards interacting with 2,2-diphenyl-1-picrylhydrazyl radical." Chemistry & Chemical Technology 10, no. 3 (September 15, 2016): 255–58. http://dx.doi.org/10.23939/chcht10.03.255.
Kaur, Jasmeet, Harsh Kumar, and Pamita Awasthi. "An Investigation on Drug Binding Ability of Cationic Surfactant CTAB." ECS Transactions 107, no. 1 (April 24, 2022): 5293–303. http://dx.doi.org/10.1149/10701.5293ecst.
La, Van N. T., and David D. L. Minh. "Bayesian Regression Quantifies Uncertainty of Binding Parameters from Isothermal Titration Calorimetry More Accurately Than Error Propagation." International Journal of Molecular Sciences 24, no. 20 (October 11, 2023): 15074. http://dx.doi.org/10.3390/ijms242015074.
udhe, Prashik B. D., and Hardik G. Bhatt. "Molecular docking studies of some novel 2 & 3-(4-aminobenzamido) benzoic acid derivatives as DHFR inhibitors for treatment of tuberculosis." International Journal of PharmTech Research 13, no. 3 (2020): 262–71. http://dx.doi.org/10.20902/ijptr.2019.130317.
Bertazzo, Martina, Dorothea Gobbo, Sergio Decherchi, and Andrea Cavalli. "Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy." Journal of Chemical Theory and Computation 17, no. 8 (July 14, 2021): 5287–300. http://dx.doi.org/10.1021/acs.jctc.1c00177.
Дисертації з теми "Standard Binding Free Energy":
Blazhynska, Marharyta. "Modeling and Standard Binding Free Energy Calculations of Complex Biological Objects." Electronic Thesis or Diss., Université de Lorraine, 2023. http://www.theses.fr/2023LORR0149.
During my thesis, I focused my research on analyzing the calculations of absolute binding free energy in protein-ligand complexes. I utilized approaches based on molecular dynamics, incorporating restraints such as alchemical and geometrical routes. My work involved studying three distinct protein-ligand complexes, contributing to the evaluation of the BFEE2 software for automating these calculations. Continuing my investigations, I applied this methodology to protein-protein interactions, which involve more complex recognition and association phenomena. I examined a specific example: a dimer of porcine insulin, where dimerization was induced by hydrophobic interactions at the interface of the monomers. Subsequently, I compared the results of calculated estimates of binding free energy with the corresponding experimental data. To deepen my understanding of binding free energy calculations in protein-ligand and protein-protein complexes, I conducted methodological research. I evaluated the robustness of the geometrical route compared to a simplified version, where additional degrees of freedom remained unrestrained during the physical separation of the partners. After demonstrating the accuracy of the geometrical route, I expanded its application to predict and evaluate the binding affinities of SARS-CoV-2 variants in interaction with a human receptor and antibodies. Additionally, I explored strategies to accelerate the calculations using the MTS option available in the Colvars module, with or without the HMR trick. By adjusting the parameters of Colvars, I achieved an almost threefold acceleration of the calculations without compromising the accuracy of the binding free energy calculations
Ranganathan, Anirudh. "Protein – Ligand Binding: Estimation of Binding Free Energies." Thesis, KTH, Skolan för kemivetenskap (CHE), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-147527.
Rocklin, Gabriel Jacob. "Predicting charged protein-ligand binding affinities using free energy calculations." Thesis, University of California, San Francisco, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3587895.
Predicting protein-ligand binding free energy from physical principles is a grand challenge in biophysics, with particular importance for drug discovery. Free energy calculations compute binding affinities by using classical mechanics to model the protein and ligand at atomic resolution, and using statistical mechanics to analyze simulations of these models. The binding affinities computed from these simulations are fully rigorous and thermodynamically correct for the model (with adequate sampling), and will agree with experimentally measured binding affinities if the model is accurate. Because free energy calculations capture the full statistical complexity of binding for flexible molecules at ambient temperature, they offer the greatest potential for quantitative accuracy of any physical method for predicting binding.
Here, I (& coauthors) present several studies relating to using free energy calculations to predict protein-ligand binding affinities for charged compounds. First, we introduce the Separated Topologies method, an approach for using free energy calculations to predict relative binding affinities of unrelated ligands. This method is useful for studying charged compounds because charged compounds are very difficult to study using absolute binding calculations, increasing the importance of relative binding calculations. Second, we use free energy calculations to predict absolute binding affinities for charged molecules to a simplified protein binding site, which is specially designed for studying charged interactions. These predictions are compared to new experimental affinity measurements and new high-resolution structures of the protein-ligand complexes. We find that all affinities are predicted to be too strong, and that this error is directly correlated with the polarity of each ligand. By uniformly weakening the strength of electrostatic interactions, we are more successful at predicting binding affinity. Third, we design and validate an analytical correction scheme to correct binding free energy calculations of ions for artifacts caused by the periodic boundary conditions employed in simulations. Fourth, we examine the sensitivity of binding affinities from free energy calculations to the force field parameters used in the simulations. This provides insight into the strength of electrostatic interactions in protein simulations, complementing our previous work comparing simulation results to experiments. Finally, we discuss potential future directions of this work.
Cabedo, Martinez Ana. "Computing free energy, binding and competition within Fragment Based Drug Discovery." Thesis, University of Southampton, 2016. https://eprints.soton.ac.uk/403850/.
Lee, Lee-Peng 1969. "Optimization of electrostatic binding free energy : application to barnase and barstar." Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/85331.
Wall, Ian. "New simulation methods for the prediction of binding free energies." Thesis, University of Southampton, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313217.
Durmaz, Vedat [Verfasser]. "Atomistic Binding Free Energy Estimations for Biological Host–Guest Systems / Vedat Durmaz." Berlin : Freie Universität Berlin, 2016. http://d-nb.info/1122111215/34.
He, Peng. "FREE ENERGY SIMULATIONS AND STRUCTURAL STUDIES OF PROTEIN-LIGAND BINDING AND ALLOSTERY." Diss., Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/531465.
Ph.D.
Protein-ligand binding and protein allostery play a crucial role in cell signaling, cell regulation, and modern drug discovery. In recent years, experimental studies of protein structures including crystallography, NMR, and Cryo-EM are widely used to investigate the functional and inhibitory properties of a protein. On the one hand, structural classification and feature identification of the structures of protein kinases, HIV proteins, and other extensively studied proteins would have an increasingly important role in depicting the general figures of the conformational landscape of those proteins. On the other hand, free energy calculations which include the conformational and binding free energy calculation, which provides the thermodynamics basis of protein allostery and inhibitor binding, have proven its ability to guide new inhibitor discovery and protein functional studies. In this dissertation, I have used multiple different analysis and free energy methods to understand the significance of the conformational and binding free energy landscapes of protein kinases and other disease-related proteins and developed a novel alchemical-based free energy method, restrain free energy release (R-FEP-R) to overcome the difficulties in choosing appropriate collective variables and pathways in conformational free energy methods like umbrella sampling and metadynamics.
Temple University--Theses
Bertazzo, Martina <1990>. "Dynamic Docking, Path Analysis and Free Energy Computation in Protein-Ligand Binding." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2020. http://amsdottorato.unibo.it/9290/1/TESI.pdf.
Alsayed, Adnan. "A government and binding approach to restrictive relatives, with particular reference to restrictive relatives in standard Arabic." Thesis, University of Essex, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243350.
Книги з теми "Standard Binding Free Energy":
Canada. The Canada-U.S. free trade agreement. Ottawa, Ont: International Trade Communications Group, 1988.
Canada. The Canada-U.S. Free Trade Agreement. Ottawa: Department of ExternalAffairs, 1988.
Canada. The Canada-U.S. free trade agreement : [text, explanatory notes]. Ottawa: External Affairs Canada, 1987.
Blaha, Stephen. The origin of the standard model: The genesis of four quark and lepton species, parity violation, the electro weak sector, color SU(3), three visible generations of fermions, and one generation of dark matter with dark energy ; Quantum theory of the third kind : a new type of divergence-free quantum field theory supporting a unified standard model of elementary particles and quantum gravity based on a new method in the calculus of variations. Auburn, NH: Pingree-Hill Publishing, 2006.
Canada. North American Free Trade Agreement between the government of the United States of America, the government of Canada, and the government of the United Mexican States. [Washington, D.C: U.S. G.P.O.], 1992.
Canada. North American Free Trade Agreement between the government of the United States of America, the government of Canada, and the government of the United Mexican States. Washington, DC: [Executive Office of the President], 1993.
E, Vance Dennis, and Vance Jean E, eds. Biochemistry of lipids, lipoproteins, and membranes. Amsterdam: Elsevier, 1991.
Canada. Pacific Salmon Treaty: Including: Yukon River agreement, revisions to December, 2002, memorandum of understanding (1985), exchange of notes--1985, 1999 & 2002. [Vancouver, B.C.?]: Pacific Salmon Commission, 2004.
Canada. Agreement amending treaty with Canada concerning Pacific Coast albacore tuna vessels and port privileges: Message from the President of the United States transmitting agreement amending treaty between the government of the United States of America and the government of Canada on Pacific Coast albacore tuna vessels and port privileges done at Washington, D.C., May 26, 1981 (The "Treaty"), effected by an exchange of diplomatic notes at Washington on July 17, 2002, and August 13, 2002 (The "Agreement"). Washington: U.S. G.P.O., 2003.
Canada. St. Lawrence Seaway: Tariff of tolls : agreement between the United States of America and Canada, amending the agreement of March 9, 1959, as amended and supplemented, effected by exchange of notes, signed at Washington June 10 and July 12, 1994, and exchange of notes, signed at Washington August 9 and October 18, 1995. Washington, D.C: Dept. of State, 2000.
Частини книг з теми "Standard Binding Free Energy":
McCammon, J. Andrew. "Free Energy and Binding Selectivity." In Computational Approaches in Supramolecular Chemistry, 515–17. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-1058-7_33.
Chattoraj, D. K., L. N. Ghosh, and P. K. Mahapatra. "Standard Free Energy of Adsorption at Liquid Interfaces." In Surfactants in Solution, 277–92. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4615-3836-3_19.
Wang, Lingle, Jennifer Chambers, and Robert Abel. "Protein–Ligand Binding Free Energy Calculations with FEP+." In Methods in Molecular Biology, 201–32. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9608-7_9.
Reif, Maria M., and Martin Zacharias. "Computational Tools for Accurate Binding Free-Energy Prediction." In Methods in Molecular Biology, 255–92. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1767-0_12.
Jespers, Willem, Johan Åqvist, and Hugo Gutiérrez-de-Terán. "Free Energy Calculations for Protein–Ligand Binding Prediction." In Methods in Molecular Biology, 203–26. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1209-5_12.
Eisenman, George, Osvaldo Alvarez, and Johan Aqvist. "Free Energy Perturbation Simulations of Cation Binding to Valinomycin." In The Pedersen Memorial Issue, 23–53. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2532-1_3.
Wong, Thomas K. F., and S. M. Yiu. "Prediction of Minimum Free Energy Structure for Simple Non-standard Pseudoknot." In Biomedical Engineering Systems and Technologies, 345–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-18472-7_27.
Aldeghi, Matteo, Joseph P. Bluck, and Philip C. Biggin. "Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner’s Guide." In Methods in Molecular Biology, 199–232. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7756-7_11.
Reddy, M. Rami, Mark D. Erion, and Atul Agarwal. "Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities." In Reviews in Computational Chemistry, 217–304. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2007. http://dx.doi.org/10.1002/9780470125939.ch4.
Mandal, Tanumoy, Andreas Ekstedt, Rikard Enberg, Gunnar Ingelman, and Johan Löfgren. "Exclusion Limits on Minimal Anomaly Free $$\mathrm {U}(1)$$ Extensions of the Standard Model." In XXII DAE High Energy Physics Symposium, 243–46. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-73171-1_55.
Тези доповідей конференцій з теми "Standard Binding Free Energy":
Chen, Kok Hao, and Jong Hyun Choi. "DNA Oligonucleotide-Templated Nanocrystals: Synthesis and Novel Label-Free Protein Detection." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11958.
Wall, Michael E. "Ligand Binding, Protein Fluctuations, And Allosteric Free Energy." In FROM PHYSICS TO BIOLOGY: The Interface between Experiment and Computation - BIFI 2006 II International Congress. AIP, 2006. http://dx.doi.org/10.1063/1.2345620.
Yue Shi, Dian Jiao, M. J. Schnieders, and Pengyu Ren. "Trypsin-ligand binding free energy calculation with AMOEBA." In 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2009. http://dx.doi.org/10.1109/iembs.2009.5335108.
Dakka, Jumana, Kristof Farkas-Pall, Matteo Turilli, David W. Wright, Peter V. Coveney, and Shantenu Jha. "Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations." In 2018 IEEE 14th International Conference on e-Science (e-Science). IEEE, 2018. http://dx.doi.org/10.1109/escience.2018.00034.
Kudrawiec, R. "The Free Exciton Binding Energy in a Strained GaN0.02As0.98 Layer." In PHYSICS OF SEMICONDUCTORS: 27th International Conference on the Physics of Semiconductors - ICPS-27. AIP, 2005. http://dx.doi.org/10.1063/1.1994105.
Takamatsu, Yuichiro. "Binding Free Energy Calculation and Structural Analysis for Antigen-Antibody Complex." In FLOW DYNAMICS: The Second International Conference on Flow Dynamics. AIP, 2006. http://dx.doi.org/10.1063/1.2204566.
Yang, Kun, Xicheng Wang, Jane W. Z. Lu, Andrew Y. T. Leung, Vai Pan Iu, and Kai Meng Mok. "A Prediction Method of Binding Free Energy of Protein and Ligand." In PROCEEDINGS OF THE 2ND INTERNATIONAL SYMPOSIUM ON COMPUTATIONAL MECHANICS AND THE 12TH INTERNATIONAL CONFERENCE ON THE ENHANCEMENT AND PROMOTION OF COMPUTATIONAL METHODS IN ENGINEERING AND SCIENCE. AIP, 2010. http://dx.doi.org/10.1063/1.3452207.
"BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2011. http://dx.doi.org/10.5220/0003167703180321.
Cain, Sahar, Ali Risheh, and Negin Forouzesh. "Calculation of Protein-Ligand Binding Free Energy Using a Physics-Guided Neural Network." In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2021. http://dx.doi.org/10.1109/bibm52615.2021.9669867.
Forouzesh, Negin. "Binding Free Energy of the Novel Coronavirus Spike Protein and the Human ACE2 Receptor." In BCB '20: 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3388440.3414712.
Звіти організацій з теми "Standard Binding Free Energy":
Midak, Lilia Ya, Ivan V. Kravets, Olga V. Kuzyshyn, Jurij D. Pahomov, Victor M. Lutsyshyn, and Aleksandr D. Uchitel. Augmented reality technology within studying natural subjects in primary school. [б. в.], February 2020. http://dx.doi.org/10.31812/123456789/3746.
Oliynyk, Kateryna, and Matteo Ciantia. Application of a finite deformation multiplicative plasticity model with non-local hardening to the simulation of CPTu tests in a structured soil. University of Dundee, December 2021. http://dx.doi.org/10.20933/100001230.
Lokke, Arnkjell, and Anil Chopra. Direct-Finite-Element Method for Nonlinear Earthquake Analysis of Concrete Dams Including Dam–Water–Foundation Rock Interaction. Pacific Earthquake Engineering Research Center, University of California, Berkeley, CA, March 2019. http://dx.doi.org/10.55461/crjy2161.