Relevant bibliographies by topics / Molecular dynamics conformational analysis

Contents

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

Academic literature on the topic 'Molecular dynamics conformational analysis'

Author: Grafiati
Published: 4 June 2025
Last updated: 1 August 2025

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Journal articles on the topic "Molecular dynamics conformational analysis"

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Krukenberg, Kristin A., Timothy O. Street, Laura A. Lavery, and David A. Agard. "Conformational dynamics of the molecular chaperone Hsp90." Quarterly Reviews of Biophysics 44, no. 2 (2011): 229–55. http://dx.doi.org/10.1017/s0033583510000314.

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AbstractThe ubiquitous molecular chaperone Hsp90 makes up 1–2% of cytosolic proteins and is required for viability in eukaryotes. Hsp90 affects the folding and activation of a wide variety of substrate proteins including many involved in signaling and regulatory processes. Some of these substrates are implicated in cancer and other diseases, making Hsp90 an attractive drug target. Structural analyses have shown that Hsp90 is a highly dynamic and flexible molecule that can adopt a wide variety of structurally distinct states. One driving force for these rearrangements is the intrinsic ATPase ac
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Ohno, Shiho, Noriyoshi Manabe, Jun Uzawa, and Yoshiki Yamaguchi. "Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and d-Arabitol by Solution NMR and Molecular Dynamics Simulations." Molecules 29, no. 5 (2024): 1072. http://dx.doi.org/10.3390/molecules29051072.

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Ribitol (C5H12O5) is an acyclic sugar alcohol that was recently identified in O-mannose glycan on mammalian α-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, d-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showe
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Garrido-Rodríguez, Pedro, Miguel Carmena-Bargueño, María Eugenia de la Morena-Barrio, et al. "Analysis of AlphaFold and molecular dynamics structure predictions of mutations in serpins." PLOS ONE 19, no. 7 (2024): e0304451. http://dx.doi.org/10.1371/journal.pone.0304451.

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Serine protease inhibitors (serpins) include thousands of structurally conserved proteins playing key roles in many organisms. Mutations affecting serpins may disturb their conformation, leading to inactive forms. Unfortunately, conformational consequences of serpin mutations are difficult to predict. In this study, we integrate experimental data of patients with mutations affecting one serpin with the predictions obtained by AlphaFold and molecular dynamics. Five SERPINC1 mutations causing antithrombin deficiency, the strongest congenital thrombophilia were selected from a cohort of 350 unrel
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Li, Xin, Na Wang, Jinyue Yang, et al. "Molecular conformational evolution mechanism during nucleation of crystals in solution." IUCrJ 7, no. 3 (2020): 542–56. http://dx.doi.org/10.1107/s2052252520004959.

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Nucleation of crystals from solution is fundamental to many natural and industrial processes. In this work, the molecular mechanism of conformational polymorphism nucleation and the links between the molecular conformation in solutions and in crystals were investigated in detail by using 5-nitrofurazone as the model compound. Different polymorphs were prepared, and the conformations in solutions obtained by dissolving different polymorphs were analysed and compared. The solutions of 5-nitrofurazone were proven to contain multiple conformers through quantum chemical computation, Raman spectra a
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Agaeva, G., G. Safarli, and N. Godjaev. "MOLECULAR MODELLİNG OF CONFORMATİONAL FLEXİBİLİTY OF HYLAMBATİN MOLECULE." Russian Journal of Biological Physics and Chemisrty 7, no. 2 (2022): 194–98. http://dx.doi.org/10.29039/rusjbpc.2022.0502.

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The features of the spatial organization of the hylambatin molecule were investigated by methods of molecular mechanics and molecular dynamics. Hylambatin consists of twelve amino acid residues in the sequence: Asp-Pro-Pro-Asp-Pro-Asn-Arg-Phe-Tyr-Gly-Met-Met-NH2. Unlike all other tachykinins, hylambatin has a Met residue replacing the usual Leu at penultimate position. The tachykinin peptide hylambatin has been isolated and chemically characterized from methanol extracts of the skin of Hylambates maculatus, an African rhacophorid frog. It has been shown that intravenously administered hylambat
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Tafi, A., Fabrizio Manetti, Federico Corelli, Stefano Alcaro, and Maurizio Botta. "Structural flexibility of hyaluronan oligomers as probed by molecular modelling." Pure and Applied Chemistry 75, no. 2-3 (2003): 359–66. http://dx.doi.org/10.1351/pac200375020359.

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In the last few years, molecular modeling studies have been published that are devoted to a better understanding of the structural flexibility of hyaluronan (HA). Further conformational investigations, however, are needed on this polysaccharide, such as the application of statistical methods to perform enhanced one-step conformational analyses of its subunits. Moreover, the adjustment of assisted model building and energy refinement (AMBER) force field could provide the appropriate computational tool to study the interactions of HA and its derivatives with proteins. The present paper reports a
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Miller, Chad, Steven Schildcrout, Howard Mettee, and Ganesaratnam Balendiran. "Molecular dynamics of fibric acids." European Journal of Chemistry 13, no. 2 (2022): 186–95. http://dx.doi.org/10.5155/eurjchem.13.2.186-195.2275.

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1H- and 13C-NMR chemical shifts were measured for four fibric acids (bezafibrate, clofibric acid, fenofibric acid, and gemfibrozil), which are lipid-lowering drugs. Correlation is found with DFT-computed chemical shifts from the conformational analysis. Equilibrium populations of optimized conformers at 298 K are very different when based on computed Gibbs energies rather than on potential energies. This is due to the significant entropic advantages of extended rather than bent conformational shapes. Abundant conformers with intramolecular hydrogen bonding via five-member rings are computed fo
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Andrałojć, Witold, Enrico Ravera, Loïc Salmon, Giacomo Parigi, Hashim M. Al-Hashimi, and Claudio Luchinat. "Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations." Physical Chemistry Chemical Physics 18, no. 8 (2016): 5743–52. http://dx.doi.org/10.1039/c5cp03993b.

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Spooner, Jacob, Heather Wiebe, Miranda Louwerse, Brandon Reader, and Noham Weinberg. "Theoretical analysis of high-pressure effects on conformational equilibria." Canadian Journal of Chemistry 96, no. 2 (2018): 178–89. http://dx.doi.org/10.1139/cjc-2017-0411.

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Along with temperature, pressure is the most important physical parameter determining the thermodynamic properties and reactivity of chemical systems. In this work, we discuss the effects of high pressure on conformational properties of organic molecules and propose an approach toward calculation of conformational volume changes based on molecular dynamics simulations. The results agree well with the experimental data. Furthermore, we demonstrate that pressure can be used as an instrument for fine-tuning of molecular conformations and to propel a properly constructed molecular rotor possessing
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Gaalswyk, Kari, and Christopher N. Rowley. "An explicit-solvent conformation search method using open software." PeerJ 4 (May 31, 2016): e2088. http://dx.doi.org/10.7717/peerj.2088.

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Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics (REMD) to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify t
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Dissertations / Theses on the topic "Molecular dynamics conformational analysis"

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Hyvönen, M. (Marja). "Molecular dynamics simulations on phospholipid membranes." Doctoral thesis, University of Oulu, 2001. http://urn.fi/urn:isbn:9514259432.

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Abstract Phospholipids are the main components of cell membranes, lipoproteins and other membrane structures in living organisms. Properties of lipid molecules are important to the overall behaviour and interactions of membranes. Furthermore, characteristics of the biological membranes act as important regulators of membrane functions. Molecular dynamics (MD) simulations were applied in this thesis to study properties of biological membranes. A certain degree of acyl chain polyunsaturation is essential for the proper functioning of membranes, but earlier MD simulations had not addressed
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Chen, Wei. "Molecular dynamics simulations of binding, unfolding, and global conformational changes of signaling and adhesion molecules." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28118.

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Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Zhu, Cheng; Committee Member: Harvey, Stephen; Committee Member: Hud, Nicholas; Committee Member: Zamir, Evan; Committee Member: Zhu, Ting.
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Atzori, Alessio. "Conformational analysis of peptides and proteins for drug design using molecular simulations." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/conformational-analysis-of-peptides-and-proteins-for-drug-design-using-molecular-simulations(050ba296-a4c4-4a5b-87bf-66d90f7ddc5a).html.

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The intrinsic plasticity of biological systems provides opportunities for rational design of selective and potent ligands. Increasingly, computational methods are being applied to predict biomolecular flexibility. However, the motions involved in these processes can be large and occur on time scales generally difficult to achieve with standard simulation methods. In order to overcome the intrinsic limitations of classical molecular dynamics, this Ph.D. project focuses on the application of advanced sampling computational techniques to capture the plasticity of diverse biological systems. The f
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Zhang, Wei. "Computational simulation of biological systems studies on protein folding and protein structure prediction /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.84Mb, 184 p, 2005. http://wwwlib.umi.com/dissertations/fullcit/3181881.

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Hafner, Melanie Salome [Verfasser]. "Structural conformational analysis of molecular dynamics of a P-glycoprotein homology model and generated intermediate structures / Melanie Salome Hafner." Bonn : Universitäts- und Landesbibliothek Bonn, 2019. http://d-nb.info/119893316X/34.

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Tippel, Franziska [Verfasser], Johannes [Akademischer Betreuer] Buchner, Michael [Gutachter] Sattler, and Johannes [Gutachter] Buchner. "Mechanistic Analysis of Conformational Dynamics of the Molecular Chaperone Hsp90 / Franziska Tippel ; Gutachter: Michael Sattler, Johannes Buchner ; Betreuer: Johannes Buchner." München : Universitätsbibliothek der TU München, 2017. http://d-nb.info/1173898832/34.

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Tippel, Franziska Verfasser], Johannes [Akademischer Betreuer] [Buchner, Michael [Gutachter] Sattler, and Johannes [Gutachter] Buchner. "Mechanistic Analysis of Conformational Dynamics of the Molecular Chaperone Hsp90 / Franziska Tippel ; Gutachter: Michael Sattler, Johannes Buchner ; Betreuer: Johannes Buchner." München : Universitätsbibliothek der TU München, 2017. http://nbn-resolving.de/urn:nbn:de:bvb:91-diss-20170217-1341437-1-7.

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Alonso, Gil Santiago. "Conformational and mechanistic analyses of α- and β-glycosidase substrates by ab initio QM/MM methods". Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/462805.

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Carbohydrates are one of the most important biochemical molecules due to their role as energetic resource for non-photosynthetic organisms, cell-cell recognition and adhesion, protection of cell membranes of bacteria and plants and ensure the proper functionality of several enzymes. Glycoproteins are important components of cell surfaces and the extracellular medium where molecular-cell interactions take place. Defects in the activity of glycoproteins are the cause of several human diseases, such as diabetes and lysosomal storage diseases. Glycoside hydrolases (GHs) are one of the most releva
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Posgai, Monica Therese. "Energetic and dynamic characterization of the IgA1:FcαRI interaction reveals long-range conformational changes in IgA1 upon receptor binding". University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1354043317.

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Bougueroua, Sana. "Caractérisation de structures explorées dans les simulations de dynamique moléculaire." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLV099/document.

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L’objectif de cette thèse est d’analyser et prédire les conformations d’un système moléculaire en combinant la théorie des graphes et la chimie computationnelle.Dans le cadre des simulations de dynamique moléculaire, une molécule peut avoir une ou plusieurs conformations au cours du temps. Dans les trajectoires de simulation de dynamique moléculaire, on peut avoir des trajectoires n’explorant qu’une seule conformation ou des trajectoires explorant plusieurs conformations, donc plusieurs transitions entre conformations sont observées. L’exploration de ces conformations dépend du temps de la sim
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Books on the topic "Molecular dynamics conformational analysis"

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Mitsuru, Nagasawa, Kurata Michio 1925-, and Toyota Conference, (1st : 1987 : Inuyama City,Japan), eds. Molecular conformation and dynamics of macromolecules in condensed systems. Elsevier, 1988.

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Keresü, G. M. Molecular mechanics and conformational analysis in drug design. Blackwell Science, 1999.

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Toyota Conference (1st 1987 Inuyama-shi, Japan). Molecular conformation and dynamics of macromolecules in condensed systems: A collection of contributions based on lectures presented at the 1st Toyota Conference, Inuyama City, Japan, 28 September-1 October 1987. Elsevier, 1988.

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Yu, Haibo. Biomolecular simulation: Inclusion of polarizability, prediction of conformational stability, and analysis of peptide folding and association. Shaker Verlag, 2004.

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Livesay, Dennis R. Protein dynamics: Methods and protocols. Humana Press, 2013.

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Dodziuk, Helena. Modern conformational analysis: Elucidating novel exciting molecular structures. VCH, 1995.

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Crippen, G. M. Distance geometry and molecular conformation. Research Studies Press, 1988.

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D, Fasman Gerald, ed. Circular dichroism and the conformational analysis of biomolecules. Plenum Press, 1996.

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D, Brasseur Robert Ph, ed. Molecular description of biological membranes by computer aided conformational analysis. CRC Press, 1990.

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Eusebio, Juaristi, ed. Conformational behavior of six-membered rings: Analysis, dynamics, and stereochemical effects. VCH, 1995.

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Book chapters on the topic "Molecular dynamics conformational analysis"

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Caves, Leo S. D., Dzung T. Nguyen, and Roderick E. Hubbard. "Conformational Variability of Insulin: a Molecular Dynamics Analysis." In Molecular Dynamics. Macmillan Education UK, 1991. http://dx.doi.org/10.1007/978-1-349-11044-5_2.

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Barnickel, G., and E. Merck. "Conformational Analysis of Peptides Using Molecular Dynamics." In Supercomputer and Chemistry. Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-75917-8_8.

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Elber, R., and M. Karplus. "Multiple Conformational States of Myoglobin: A Molecular Dynamics Analysis." In Structure, Dynamics and Function of Biomolecules. Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-71705-5_4.

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Frank, Martin. "Conformational Analysis of Oligosaccharides and Polysaccharides Using Molecular Dynamics Simulations." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2343-4_22.

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Jørgensen, Flemming Steen, Inge Thøger Christensen, and Anja Rabijns. "From Cyclohexane to FK506 — Conformational Analysis by Molecular Dynamics." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_9.

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Hruby, Victor J., Wieslaw Kazmierski, B. Montgomery Pettitt, and Fahad Al-Obeidi. "Conformational Constraints in the Design of Receptor Selective Peptides: Conformational Analysis and Molecular Dynamics." In Molecular Biology of Brain and Endocrine Peptidergic Systems. Springer US, 1988. http://dx.doi.org/10.1007/978-1-4684-8801-2_2.

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Deuflhard, Peter. "From Molecular Dynamics to Conformation Dynamics in Drug Design." In Trends in Nonlinear Analysis. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05281-5_6.

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Toro-Labbe, A., and J. Maruani. "Symmetry Analysis and Conformational Dependence of The Properties of Rigid Molecules Embedded in Crystal Sites." In Structure and Dynamics of Molecular Systems. Springer Netherlands, 1986. http://dx.doi.org/10.1007/978-94-009-4662-0_2.

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Scheraga, Harold A. "Conformational Analysis of Polypeptides and Proteins for the Study of Protein Folding, Molecular Recognition, and Molecular Design." In Structure and Dynamics of Nucleic Acids, Proteins, and Membranes. Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5308-9_1.

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Hamrick, Grayson S., Casey H. Londergan, and Louise K. Charkoudian. "Heterologous Expression, Purification, and Characterization of Type II Polyketide Synthase Acyl Carrier Proteins." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2273-5_13.

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AbstractThe enzymes that comprise type II polyketide synthases (PKSs) are powerful biocatalysts that, once well-understood and strategically applied, could enable cost-effective and sustainable access to a range of pharmaceutically relevant molecules. Progress toward this goal hinges on gaining ample access to materials for in vitro characterizations and structural analysis of the components of these synthases. A central component of PKSs is the acyl carrier protein (ACP), which serves as a hub during the biosynthesis of type II polyketides. Herein, we share methods for accessing type II PKS A
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Conference papers on the topic "Molecular dynamics conformational analysis"

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Sauer, M., K. H. Drexhage, K. T. Han, S. Nord, and C. Zander. "Following the Dynamics of Single Oligonucleotide Molecules in Water." In Laser Applications to Chemical and Environmental Analysis. Optica Publishing Group, 1998. http://dx.doi.org/10.1364/lacea.1998.lmc.14.

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The dynamic fluorescence characteristics of individual dye molecules in specific local environment are of particular interest for many biological applications.1,2 Furthermore, dye molecules that are influenced by the environment can act as molecular probes, i. e. they exhibit information about neighbouring groups and changes in the microenvironment. They also allow the direct observation of individual dynamic events such as conformational changes of a biological macromolecule if they are monitored on the single-molecule level. In addition, measurements on individual molecules are well suited f
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Fantucci, P., T. Marino, N. Russo, and A. M. Villa. "Conformational analysis of dolastatin 10 and dolastatin 15 by molecular mechanics and molecular dynamics." In The first European conference on computational chemistry (E.C.C.C.1). AIP, 1995. http://dx.doi.org/10.1063/1.47720.

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Meddeb, S., J. Ph Demaret, J. P. Ballini, et al. "Conformational analysis of a family of potent antithrombotic peptides using high temperature molecular dynamics." In The first European conference on computational chemistry (E.C.C.C.1). AIP, 1995. http://dx.doi.org/10.1063/1.47797.

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Mukherjee, Rudranarayan M., Paul Crozier, and Kurt S. Anderson. "Multibody Molecular Dynamics II: Applications and Results." In ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/detc2007-35561.

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This is the second paper in a series of two papers on using multibody dynamics algorithms and methods for coarse grained molecular dynamics simulations. In the previous paper, the theoretical discussions on this topic have been presented. This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include water boxes, alkane chains, alanine dipeptide and carboxyl terminal fragments of Calmodulin, Ribosomal, and Rhodopsin proteins. The atomistic representations of these systems include several thousand deg
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Makarov, Gennady, Olga Borodina, Artem Masunov, et al. "Combined approach to conformational analysis of 4-hydroxyproline containing podands using NMR and molecular dynamics simulation." In ACTUAL PROBLEMS OF ORGANIC CHEMISTRY AND BIOTECHNOLOGY (OCBT2020): Proceedings of the International Scientific Conference. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0069420.

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Duan, Shanzhong, and Andrew Ries. "An Efficient O(N) Algorithm for Computer Simulation of Rigid Body Molecular Dynamics." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-42032.

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Molecular dynamics is effective for a nano-scale phenomenon analysis. There are two major computational costs associated with computer simulation of atomistic molecular dynamics. They are calculation of the interaction forces and formation/solution of equations of motion. In this paper, an O(N) (order N) procedure is presented for calculation of the interaction forces and formation/solution of equations of motion. For computational costs associated with potentials or interaction forces, an internal coordinate method is used. Use of the internal coordinate method makes application of multi-rigi
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Maftouni, N., M. Amininasab, and F. Kowsari. "Pressure Field in Liquid Phase Nanomembrane System." In ASME 2010 10th Biennial Conference on Engineering Systems Design and Analysis. ASMEDC, 2010. http://dx.doi.org/10.1115/esda2010-25234.

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Nanomembrane is a very important part of living systems. Alive cells have lipid bilayer nanomembrane in liquid phase. The lateral pressure profile, or stress profile, across a cell nanomembrane is the result of the inhomogeneous nature of the interactions within a nanomembrane. It has been shown that the work exerted by the pressure profile when a protein conformational change takes place is significant, of the order of 10kBT, and that the lateral pressure profile averaged over the whole nanomembrane is modified by the inclusion of a protein. Indeed, understanding the full coupling for stress
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Harada, Ryuhei, Yasutaka Nishihara, Nobuhiko Wakai, and Akio Kitao. "Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2014 (ICCMSE 2014). AIP Publishing LLC, 2014. http://dx.doi.org/10.1063/1.4897682.

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Hwang, Wonmuk, and Matthew J. Lang. "Mechanism of Force Generation in Kinesin Motility." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-175543.

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Conventional kinesin is a dimeric motor protein that uses adenosine triphosphate (ATP) to walk processively along the microtubule. Although its nucleotide dependent conformational switching and binding of the neck linker (NL) on the motor head are known to be key events in kinesin motility, the basic mechanism by which it amplifies a small conformational change upon ATP binding to generate the force of the walking stroke has not been known. We combined structural analysis with a set of molecular dynamics simulations to identify the 9-residue long N-terminal region, which we named the ‘cover st
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Moorthy, Narayana Subbiah Hari Narayana, Chandrabose Karthikeyan, and Elangovan Manivannan. "Molecular Dynamic Simulations-Based Conformational Analysis and Binding Study of CP-225917 on Farnesyl Transferase Enzyme." In ECMC 2022. MDPI, 2022. http://dx.doi.org/10.3390/ecmc2022-13427.

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Reports on the topic "Molecular dynamics conformational analysis"

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Rinderspacher, Berend C., Jaydeep P. Bardhan, and Ahmed E. Ismail. Wavelet Analysis for Molecular Dynamics. Defense Technical Information Center, 2015. http://dx.doi.org/10.21236/ada619816.

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Picard, Richard Roy, and Kabekode Ghanasham Bhat. Sensitivity Analysis and Uncertainty Quantification for the LAMMPS Molecular Dynamics Simulation Code. Office of Scientific and Technical Information (OSTI), 2017. http://dx.doi.org/10.2172/1372820.

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Liu, Xiang-Yang, and Anders David Andersson. Monte Carlo analysis: error of extrapolated thermal conductivity from molecular dynamics simulations. Office of Scientific and Technical Information (OSTI), 2016. http://dx.doi.org/10.2172/1331293.

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Bhatia, Harsh, Attila Gyulassy, Mitchell Ong, et al. Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics. Office of Scientific and Technical Information (OSTI), 2016. http://dx.doi.org/10.2172/1331475.

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Slapikas, Robert, Anindya Ghoshal, Luis Bravo, Muthuvel Murugan, and Douglas Wolfe. Molecular Dynamics Analysis and Optimization of Ultra-High-Temperature Ceramic (UHTC)Compositions for Propulsion. DEVCOM Army Research Laboratory, 2022. http://dx.doi.org/10.21236/ad1171344.

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Ruangpornvisuti, Vithaya. A Study of conformational equilibrium of semicarbazone derivatives and their complexes with cations : research report. Chulalongkorn University, 2006. https://doi.org/10.58837/chula.res.2006.36.

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The structure optimizations of picolinaldehyde N-oxide thiosemicarbazone (Hpiotsc), 2-benzoylpyridine semicarbazone (H2BzPS), their imino tautomers and their complexes with Ni(II), Cu(II) and Zn(II) were carried out using DFT calculations at the B3LYP/LANL2DZ level of theory. Thermodynamic properties of tautomerizations of Hpiotsc and H2BzPS and complexations of their complexes derived from the frequency calculations at the same level were obtained. The B3LYP/LANL2DZ-optimized geometry parameters for the complexes of [[Ni(Hpiotsc)[subscript 2]][superscript 2+]], [Cu(Hpiotsc).Cl[subscript 2]] a
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Hosen, Md Tofazzal. Analysis of Bioactive Phytomolecules from Aegle marmelos (Bael) Utilizing Molecular Dynamics Simulation and Pharmacoinformatics for Treating HER2-Positive Gastric Carcinoma. ResearchHub Technologies, Inc., 2025. https://doi.org/10.55277/researchhub.jjvyv35s.

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Pianwanit, Somsak, and Sirirat Kokpol. Theoretical analysis of photoinduced electron transfer in FMN binding protein : Effect of changes in one charge on electron transfer rate. Chulalongkorn University, 2013. https://doi.org/10.58837/chula.res.2013.32.

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Photoinduced electron transfer (PET) is an important process due to its several applications, e.g. solar energy conversion. Flavoproteins are generally selected as a model for the study of PET. In this research, effect of charge at residue 13 on the PET from Trp32, Tyr35 and Try106 to an excited isoalloxazine (Iso*) in FMN binding protein (FBP) from Desulfovibrio vulgaris (Miyazaki F) was studied. A wild type (E13 with negative charge) and four mutations of FBP at residue 13, E13K and E13R (politive charge), E13T and E13Q (neutral charge), were subjected to molecular dynamics (MD) simulations,
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Casey, Therese, Sameer J. Mabjeesh, Avi Shamay, and Karen Plaut. Photoperiod effects on milk production in goats: Are they mediated by the molecular clock in the mammary gland? United States Department of Agriculture, 2014. http://dx.doi.org/10.32747/2014.7598164.bard.

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US scientists, Dr. Theresa Casey and Dr. Karen Plaut, collaborated with Israeli scientists, Dr. SameerMabjeesh and Dr. AviShamay to conduct studies proposed in the BARD Project No. US-4715-14 Photoperiod effects on milk production in goats: Are they mediated by the molecular clock in the mammary gland over the last 3 years. CLOCK and BMAL1 are core components of the circadian clock and as heterodimers function as a transcription factor to drive circadian-rhythms of gene expression. Studies of CLOCK-mutant mice found impaired mammary development in late pregnancy was related to poor lactation p
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Sessa, Guido, and Gregory Martin. role of FLS3 and BSK830 in pattern-triggered immunity in tomato. United States Department of Agriculture, 2016. http://dx.doi.org/10.32747/2016.7604270.bard.

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Pattern-recognition receptors (PRRs) located on the plant cell surface initiate immune responses by perceiving conserved pathogen molecules known as pathogen-associated molecular patterns (PAMPs). PRRs typically function in multiprotein complexes that include transmembrane and cytoplasmickinases and contribute to the initiation and signaling of pattern-triggered immunity (PTI). An important challenge is to identify molecular components of PRR complexes and downstream signaling pathways, and to understand the molecular mechanisms that mediate their function. In research activities supported by
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