Relevant bibliographies by topics / Carbohydrate force field

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Carbohydrate force field'

Author: Grafiati
Published: 5 June 2025
Last updated: 1 August 2025

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Journal articles on the topic "Carbohydrate force field"

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Guvench, Olgun, Devon Martin, and Megan Greene. "Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins." International Journal of Molecular Sciences 23, no. 1 (2021): 473. http://dx.doi.org/10.3390/ijms23010473.

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The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the qua
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Jaya, krishna Koneru, and Mondal Jagannath. "Quantitative assessment of amylose dimerization process across force fields." Journal of Indian Chemical Society Vol. 96, Jul 2019 (2019): 949–56. https://doi.org/10.5281/zenodo.5644752.

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Tata Institute of Fundamental Research, Centre for Interdisciplinary Science, 36/P Gopanapalli Village, Serillingampally, Hyderabad-500 107, Telangana, India <em>E-mail</em>: jmondal@tifrh.res.in <em>Manuscript received online 10 May 2019, revised and accepted 23 May 2019</em> Despite being a key biomacromolecule, carbohydrate has received much less attention from computational community, compared to protein and lipids. This is majorly because of slow development of classical force fields for carbohydrate due to associated complexity in sampling its intrinsic flexibility and lack of an extensi
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Spiwok, Vojtěch, Petra Lipovová, Tereza Skálová, et al. "Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance." Journal of Computer-Aided Molecular Design 19, no. 12 (2006): 887–901. http://dx.doi.org/10.1007/s10822-005-9033-z.

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Grootenhuis, Peter D. J., and Cornelis A. G. Haasnoot. "A CHARMm Based Force Field for Carbohydrates Using the CHEAT Approach: Carbohydrate Hydroxyl Groups Represented by Extended Atoms." Molecular Simulation 10, no. 2-6 (1993): 75–95. http://dx.doi.org/10.1080/08927029308022160.

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Guvench, Olgun, Sairam S. Mallajosyula, E. Prabhu Raman, et al. "CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling." Journal of Chemical Theory and Computation 7, no. 10 (2011): 3162–80. http://dx.doi.org/10.1021/ct200328p.

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Stroylov, Victor, Maria Panova, and Philip Toukach. "Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations." International Journal of Molecular Sciences 21, no. 20 (2020): 7626. http://dx.doi.org/10.3390/ijms21207626.

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Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular dynamics (MD) trajectories and their comparison to the published experimental data. Using various ranking schemes, it was concluded that explicit solvent MM3 MD yielded non-inferior NOE
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Chen, Yanan, Harindra Vedala, Gregg P. Kotchey, et al. "Detection of Lectins using Glyco-Functionalized Nanosensors." MRS Proceedings 1451 (2012): 191–96. http://dx.doi.org/10.1557/opl.2012.1291.

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ABSTRACTWe have used single-walled carbon nanotube field-effect transistor (SWNT-FET) and chemically converted graphene field-effect transistor (CCG-FET) devices to probe the interactions between carbohydrates and their recognition lectins. Porphyrin- and pyrene-based glycoconjugates were used as receptor molecules and the target lectins were two bacterial lectins that present different carbohydrate preference, namely PA-IL, PA-IIL from Pseudomonas aeruginosa and a plant lectin Concanavalin A. The specific binding between lectin and carbohydrate can be transduced to the change in FET device co
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Balogh, Gábor, Tamás Gyöngyösi, István Timári, et al. "Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides." Journal of Chemical Information and Modeling 59, no. 11 (2019): 4855–67. http://dx.doi.org/10.1021/acs.jcim.9b00666.

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Pandey, Poonam, Asaminew H. Aytenfisu, Alexander D. MacKerell, and Sairam S. Mallajosyula. "Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives." Journal of Chemical Theory and Computation 15, no. 9 (2019): 4982–5000. http://dx.doi.org/10.1021/acs.jctc.9b00327.

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Panczyk, Tomasz, Wojciech Plazinski, François-Yves Dupradeau, Agnieszka Brzyska, and Pawel Wolski. "Interaction of Chondroitin and Hyaluronan Glycosaminoglycans with Surfaces of Carboxylated Carbon Nanotubes Studied Using Molecular Dynamics Simulations." Molecules 28, no. 2 (2023): 826. http://dx.doi.org/10.3390/molecules28020826.

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Interaction of β-D-glucopyranuronic acid (GlcA), N-acetyl-β-D-glucosamine (GlcNAc), N-acetyl-β-D-galactosamine (GalNAc) and two natural decameric glycosaminoglycans, hyaluronic acid (HA) and Chondroitin (Ch) with carboxylated carbon nanotubes, were studied using molecular dynamics simulations in a condensed phase. The force field used for carbohydrates was the GLYCAM-06j version, while functionalized carbon nanotubes (fCNT) were described using version two of the general amber force field. We found a series of significant differences in carbohydrate-fCNT adsorption strength depending on the mo
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Dissertations / Theses on the topic "Carbohydrate force field"

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Fourie, Alexander Rees. "Computational analysis of Escherichia coli O25 and O25b carbohydrate antigens using the CHARMM36 and GLYCAM06 force fields." Master's thesis, Faculty of Science, 2020. http://hdl.handle.net/11427/32264.

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The emergence of ST131 extra-intestinal pathogenic Escherichia coli that are resistant to multiple antibiotics is a growing international health concern. Infections are common, treatment options for antibiotic resistant bacteria are limited and there is no vaccine available. Polysaccharides serve key functions in immune response to bacterial infection. The Opolysaccharides present on the cell surface of gram negative bacteria are antigenic and are associated with specific bacterial serogroups. These are, therefore, a potentially effective target for vaccines. Most ST131 E. coli isolates expres
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Rhoad, Jonathan S. "DNA-binding carbohydrates for coordination to a photoactive dirhodium complex and molecular dynamics studies of methyl furanosides: evaluation of available force fields." The Ohio State University, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=osu1101315894.

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Rhoad, Jonathan Sidney. "DNA-binding carbohydrates for coordination to a photoactive dirhodium complex and molecular dynamics studies of methyl furanosides evaluation of available force fields /." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1101315894.

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Thesis (Ph. D.)--Ohio State University, 2004.<br>Title from first page of PDF file. Document formatted into pages; contains xviii, 160 p.; also includes graphics Includes bibliographical references (p. 117-120). Available online via OhioLINK's ETD Center
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Books on the topic "Carbohydrate force field"

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Keith, Lierre. The vegetarian myth: Food, justice and sustainability. Flashpoint Press, 2009.

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Gonder, Ulrike, ed. Ethisch Essen mit Fleisch: Eine Streitschrift über nachhaltige und ethische Ernährung mit Fleisch und die Missverständnisse und Risiken einer streng vegetarischen und veganen Lebensweise. Riva, 2021.

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El mito vegetariano: Comida, Justicia, Sostenibilidad. Capitán Swing Libros, 2018.

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Le Mythe végétarien: Nourriture, justice et pérennité. Les Editions Pilule Rouge, 2013.

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Keith, Lierre. Vegetarian Myth: Food, Justice, and Sustainability. PM Press, 2010.

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El Mito Vegetariano: Alimento, justicia y sustentabilidad. FisicalBook, 2012.

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Keith, Lierre. Vegetarian Myth: Food, Justice, and Sustainability. PM Press, 2009.

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Keith, Lierre. The Vegetarian Myth: Food, Justice, and Sustainability. ReadHowYouWant, 2013.

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Book chapters on the topic "Carbohydrate force field"

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Tschampel, Sarah M., Karl N. Kirschner, and Robert J. Woods. "Incorporation of Carbohydrates into Macromolecular Force Fields: Development and Validation." In ACS Symposium Series. American Chemical Society, 2006. http://dx.doi.org/10.1021/bk-2006-0930.ch013.

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Richards, Nigel G. J. "An Introduction to the Theoretical Basis of Semi-Empirical Quantum-Mechanical Methods for Biological Chemists." In Molecular Orbital Calculations for Biological Systems. Oxford University Press, 1998. http://dx.doi.org/10.1093/oso/9780195098730.003.0007.

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Computational methods that can be employed to investigate fundamental questions concerning the complex chemical and structural behavior of biological molecules such as proteins, carbohydrates, and nucleic acids have been traditionally limited by the large number of atoms that comprise even the simplest system of biochemical interest. As a consequence, highly parameterized, empirical force field methods have been developed that describe the energy of macromolecular structures as a function of the spatial locations of the atomic nuclei. In combination with algorithms for simulating molecular dyn
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Conference papers on the topic "Carbohydrate force field"

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Stadler, Reinhard, Wolfram Fuerbeth, Mariel Grooters, Claudia Janosch, Andrzej Kuklinski, and Wolfgang Sand. "Studies on the Application of Microbially Produced Polymeric Substances as Protecting Layers against Microbially Influenced Corrosion of Iron and Steel." In CORROSION 2010. NACE International, 2010. https://doi.org/10.5006/c2010-10209.

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Abstract The contribution of biofilms to corrosion of metals and alloys, termed microbially influenced corrosion (MIC), is still a challenge for research in the field of corrosion protection. In order to inhibit or prevent MIC, one promising route can be to inhibit the adhesion of single cells. The processes of adhesion and desorption of microorganisms are known to be induced and mediated by various (bio-)molecules. The aim of this project is to identify and to investigate substances appropriate to inhibit the formation of biofilms of sulphate reducing bacteria (SRB). For this purpose, so-call
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Rasmussen, Kjeld. "OPTIMIZED CONSISTENT FORCE FIELD FOR SACCHARIDES." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.547.

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Jewel, Yead, Prashanta Dutta, and Jin Liu. "Coarse-Grained Molecular Dynamics Simulations of Sugar Transport Across Lactose Permease." In ASME 2015 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/imece2015-52337.

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Sugar (one of the critical nutrition elements for all life forms) transport across the cell membranes play essential roles in a wide range of living organism. One of the most important active transport (against the sugar concentration) mechanisms is facilitated by the transmembrane transporter proteins, such as the Escherichia coli lactose permease (LacY) proteins. Active transport of sugar molecules with LacY proteins requires a proton gradient and a sequence of complicated protein conformational changes. However, the exact molecular mechanisms and the protein structural information involved
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Engelsen, Soren B., Daniel E. Madsen, Anders L. Esbensen, Lars Olsen, and Lars Hemmingsen. "VALIDATION OF CARBOHYDRATE FORCE FIELDS. DENSITY FUNCTIONAL AND AB INITIO METHODS." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.388.

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Kouwijzer, M. L. C. E., B. P. van Eijck, H. Kooijman та J. Kroon. "Extension of the gromos force field for carbohydrates, resulting in improvement of the crystal structure determination of α-D-galactose". У The first European conference on computational chemistry (E.C.C.C.1). AIP, 1995. http://dx.doi.org/10.1063/1.47730.

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Mathew, Anil, Mitch Crook, Keith Chaney, and Andrea Humphries. "Bioethanol Production From Canola Straw Using a Continuous Flow Immobilized Cell System." In ASME 2012 6th International Conference on Energy Sustainability collocated with the ASME 2012 10th International Conference on Fuel Cell Science, Engineering and Technology. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/es2012-91061.

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Global cultivation of canola increased by approximately 22% between 2000 and 2009, due to increased demand for canola oil for biodiesel production and as an edible oil. In 2009 over 290,000 km2 of canola was cultivated globally. In contrast to oilseed, the commercial market for canola straw is minimal and it is generally ploughed back into the field. The high carbohydrate content (greater than 50 % by dry weight) of canola straw suggests it would be a good feedstock for second-generation bioethanol production. There are four major steps involved in bioethanol production from lignocellulosic ma
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