Relevant bibliographies by topics / CHARMM

Contents

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

Academic literature on the topic 'CHARMM'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 July 2025

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Journal articles on the topic "CHARMM"

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Jo, Sunhwan, Taehoon Kim, Vidyashankara G. Iyer, and Wonpil Im. "CHARMM-GUI: A web-based graphical user interface for CHARMM." Journal of Computational Chemistry 29, no. 11 (2008): 1859–65. http://dx.doi.org/10.1002/jcc.20945.

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Brooks, B., and R. Venable. "CHARMM for Molecular Simulations." ACM SIGBIO Newsletter 8, no. 3 (1986): 30–34. http://dx.doi.org/10.1145/16297.992728.

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Shaw, Robert A., Tristan Johnston-Wood, Benjamin Ambrose, Timothy D. Craggs, and J. Grant Hill. "CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field." Journal of Chemical Theory and Computation 16, no. 12 (2020): 7817–24. http://dx.doi.org/10.1021/acs.jctc.0c00721.

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Nguyen, Trang Truc, Man Hoang Viet, and Mai Suan Li. "Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase." Scientific World Journal 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/536084.

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The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energyΔGbindof oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus.ΔGbindis estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding
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Park, Sang-Jun, Hugo Guterres, Han Zhang, and Wonpil Im. "CHARMM-GUI high-throughput simulator." Biophysical Journal 121, no. 3 (2022): 531a. http://dx.doi.org/10.1016/j.bpj.2021.11.2800.

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Cheng, Xi, Yifei Qi, Jumin Lee, Sunhwan Jo, and Wonpil Im. "CHARMM Gui Membrane Builder Updates." Biophysical Journal 108, no. 2 (2015): 159a. http://dx.doi.org/10.1016/j.bpj.2014.11.877.

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Brooks, B. R., C. L. Brooks, A. D. Mackerell, et al. "CHARMM: The biomolecular simulation program." Journal of Computational Chemistry 30, no. 10 (2009): 1545–614. http://dx.doi.org/10.1002/jcc.21287.

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Park, Sang-Jun, Hyuntae Na, and Wonpil Im. "CHARMM-GUI normal mode analyzer." Biophysical Journal 123, no. 3 (2024): 283a. http://dx.doi.org/10.1016/j.bpj.2023.11.1759.

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Kim, Seonghoon, Jumin Lee, Sunhwan Jo, Charles L. Brooks, Hui Sun Lee, and Wonpil Im. "CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules." Journal of Computational Chemistry 38, no. 21 (2017): 1879–86. http://dx.doi.org/10.1002/jcc.24829.

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Kim, Seonghoon, Jumin Lee, Sunhwan Jo, and Wonpil Im. "CHARMM-GUI Ligand Reader & Modeler." Biophysical Journal 112, no. 3 (2017): 289a. http://dx.doi.org/10.1016/j.bpj.2016.11.1564.

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Dissertations / Theses on the topic "CHARMM"

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Painter, Gallia Marie. "Multiscale Modeling of Polymer Bond Scission." Case Western Reserve University School of Graduate Studies / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=case1247171422.

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Cisse, Cheickna. "Etude structurale des aptamères peptidiques anti-Fur et de leur interaction avec leur cible." Phd thesis, Université de Grenoble, 2012. http://tel.archives-ouvertes.fr/tel-00846781.

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Fur (Ferric Uptake Regulator) est un régulateur transcriptionnel spécifique des bactéries qui intervient dans le contrôle de l'homéostasie du fer, ce qui en fait une cible antibactérienne intéressante. Avant mon arrivée au laboratoire, quatre inhibiteurs interagissant spécifiquement avec Fur avaient été isolés. La partie active de ces inhibiteurs consiste en des peptides de 13 acides aminés. Au cours de cette thèse, j'ai utilisé une double-approche : théorique et expérimentale pour étudier l'interaction de ces peptides avec Fur afin de comprendre le mécanisme d'inhibition. J'ai synthétisé plus
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Åkesson, Patrik. "Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-103688.

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A great interest has been shown for self-assembled organic nano-structures that can be used in a variety of optoelectronic applications, from element detection to home electronics. It is known from experimental research that sexiphenyl (6P) grown on muscovite mica substrate form uniaxially self-assembled nanofibers which together with sexithiophene (6T) deposited on top gives the possibility to tune their polarized emission. A key to continue develop and explore the full potential of this technique is to understand the mechanisms behind the growth. This thesis investigate the initial growth of
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Smith, Addison Kyle. "Molecular Dynamic Simulation of Protein Devices and the Parameterization of Azides and Alkynes for Use in Unnatural Amino Acid Models." BYU ScholarsArchive, 2021. https://scholarsarchive.byu.edu/etd/8783.

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Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and diagnostics -- these unique proteins are called protein devices. Current techniques can perform these functionalizations at a specific residue on the protein, but what remains is identifying what happens to protein structure when mutated, and where to perform the attachment. Both of these issues can be examined using molecular dynamic (MD) simulations. Currently, simulations of the unnatural amino acid (uAA) mutations necessary for protein device func
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Sawert, David, Holmes Oskar Anderhagen, and Aron Johanson. "Analys av Organiska Molekyler i Mikroskopiska Vattendroppar." Thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-415316.

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The aim of the study was to analyse where different organic molecules situated themselves in relation to the water surface of a water microdroplet and use the resulting data to compare three different forcefields in the simulation package GROMACS. The forcefields used were: General AMBER forcefield (GAFF), Optimized potentials for liquid simulations - all atoms (OPLS-AA), and CHARMM general force field (CGenFF). A library of 146 molecules were simulated using molecular dynamics. Out of the 146 molecules only 65 resulted in useful data for the comparison of the forcefields. The molecules were p
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Godfrey, I. M. "Charm photoproduction at threshold and 20 GeV charmed particle delay." Thesis, Imperial College London, 1987. http://hdl.handle.net/10044/1/38332.

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Magneville, Christophe. "Étude de la photoproduction du charme, désintégrations et temps de vie du méson charmé-étrange." Paris 11, 1987. http://www.theses.fr/1987PA112358.

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Davis, Adam C. "Search for Mixing and Charge Parity Violation in Neutral Charm Mesons through Semileptonic B Meson Decay." University of Cincinnati / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1470671480.

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Debu, Pascal. "Résultats de l'expérience Beam Dump réalisée au CERN en 1982." Paris 11, 1985. http://www.theses.fr/1985PA112138.

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Nous décrivons la mesure des taux d’interactions à courant chargé dans le fer des νμ, ν̅μ et (ν̅e) d’énergie supérieure à 20 Gev dans le détecteur de la collaboration CHDS au CERN. Ces neutrinos ont été produits lors du déversement de protons de 400 Gev/c sur des cibles de cuivre de densités différentes (« beam dump 1982 »). En extrapolant les mesures à une cible de densité infinie, nous déterminons les taux d’interactions des neutrinos directs (i. E. Produits soit directement, soit lors de la désintégration de particules à très courte durée de vie). Ils sont tous significativement différents
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Tran, Ngoc Tiem. "Recherche des oscillations de neutrinos par apparition du τ avec désintégration muonique du vτ dans l’expérience OPERA". Thesis, Lyon 1, 2010. http://www.theses.fr/2010LYO10203/document.

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La physique des oscillations de neutrinos occupe une place majeure dans les études s’intéressant à cetteparticule. Le mécanisme des oscillations, basé sur un changement d’état de saveur d’un neutrino durant sapropagation, permet d’élucider les déficits observés de neutrinos solaires et atmosphériques et apporte des indicationsintéressantes de physique au delà du Modèle Standard par l'étude des angles de mélanges et du schéma de masse desneutrinos.OPERA est un détecteur hybride combinant à la fois latechnique d'une détection électronique en temps réel et la technique de la chambre à brouillard
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Books on the topic "CHARMM"

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Yi, Yun-ho. Chaebŏl ŭi chaemu kujo wa chagŭm chodal. Nanam Chʻulpʻan, 2005.

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Hoàng, Minh Quốc. The charm of Vietnam =: Le charme du Việt Nam = Việt Nam quyé̂n rũ. VNA Pub. House, 2011.

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Robertson, Sophie. Charms. Guild of Master Craftsman Publications, 2013.

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Kamermans, Johan. Verglaasde charme: De schoonheid van de Nederlandse tegel = Glazed charm : the beauty of Dutch tiles. SPA, 2013.

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Hart, Kendall. Charm! Hyperion Books, 2008.

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Li, Charles N. Charm! Hyperion, 2008.

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MacLean, Robert. Charm. Baker's Plays, 1999.

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Propertius, Sextus. Charm. Sun & Moon Press, 1995.

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Stillings, Marianne. Killer charms. Avon Books, 2008.

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Simmons, Trana Mae. Southern charms. Jove, 1999.

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Book chapters on the topic "CHARMM"

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Rone, Rebecca, Frank A. Momany, and Mary Dygert. "Conformational studies on vancomycin using QUANTA/CHARMm." In Peptides. Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2264-1_108.

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Kamberaj, Hiqmet. "Python Interactive GUI for CHARMM Software Package." In Computer Simulations in Molecular Biology. Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-34839-6_9.

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Mallajosyula, Sairam S., Sunhwan Jo, Wonpil Im, and Alexander D. MacKerell. "Molecular Dynamics Simulations of Glycoproteins Using CHARMM." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2343-4_25.

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Li, Yupeng, Jinchan Liu, and James C. Gumbart. "Preparing Membrane Proteins for Simulation Using CHARMM-GUI." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1394-8_13.

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Mesirov, Jill P., Pablo Tamayo, and Robert J. Nagle. "On the Parallelization of CHARMM on the CM-5/5E." In Mathematical Approaches to Biomolecular Structure and Dynamics. Springer New York, 1996. http://dx.doi.org/10.1007/978-1-4612-4066-2_11.

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Hodošček, M., E. M. Billings, T. E. Cheatham, and B. R. Brooks. "High Performance Computing in Biophysics: Recent Experiences and Developments of Charmm." In Astrophysics and Space Science Library. Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0864-8_16.

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MacKerell, Alexander D., and Lennart Nilsson. "Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using Charmm." In Computational Studies of RNA and DNA. Springer Netherlands, 2006. http://dx.doi.org/10.1007/978-1-4020-4851-3_3.

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Lagant, P., D. Nolde, and G. Vergoten. "Inclusion of a modified Urey-Bradley type force field in the Charmm program." In Spectroscopy of Biological Molecules: New Directions. Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4479-7_183.

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Ullmann, G. M., I. Muegge, and E. W. Knapp. "Shifts of the Special Pair Redox Potential of Mutants of Rhodobacter sphaeroides Calculated with DelPhi and CHARMM Energy Functions." In The Reaction Center of Photosynthetic Bacteria. Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-642-61157-5_12.

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Momany, Frank A., V. Joseph Klimkowski, and Lothar Schäfer. "On the use of conformationally dependent geometry trends from ab initio studies to determine empirical parameters for the CHARMm molecular mechanics force field." In Proteins. Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-010-9063-6_57.

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Conference papers on the topic "CHARMM"

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Sukhwani, Bharat, and Martin C. Herbordt. "FPGA-based acceleration of CHARMM-potential minimization." In the Third International Workshop. ACM Press, 2009. http://dx.doi.org/10.1145/1646461.1646462.

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Taufer, M., E. Perathoner, A. Cavalli, A. Caflisch, and T. Stricker. "Performance characterization of a molecular dynamics code on PC clusters: is there any easy parallelism in CHARMM?" In Proceedings 16th International Parallel and Distributed Processing Symposium. IPDPS 2002. IEEE, 2002. http://dx.doi.org/10.1109/ipdps.2002.1015505.

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Ganesan, Narayan, Michela Taufer, Brad Bauer, and Sandeep Patel. "FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME." In Distributed Processing, Workshops and Phd Forum (IPDPSW). IEEE, 2011. http://dx.doi.org/10.1109/ipdps.2011.187.

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Kralj, Sebastjan, Milan Hodošček, Marko Jukić, and Urban Bren. "A comprehensive in silico protocol for fast automated mutagenesis and binding affinity scoring of protein-ligand complexes." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.674k.

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Protein-protein interactions (PPI) are critical for cellular functions, host-pathogen dynamics and are crucial with drug design efforts. The interaction of proteins is dependent on the amino acid sequence of a protein as it determines its binding affinity to various molecules, including drugs, DNA, RNA, and proteins. Polymorphisms, natural DNA variations, affect PPIs by altering protein structure and stability. Computational chemistry is vital for the prediction of ligand-protein interactions through techniques such as docking and molecular dynamics and can elucidate the changes in energy asso
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Hidayat, Riyan, Lutfi Rohman, and Artoto Arkundato. "The target of SARS-CoV-2: Analysis of N3 ligand binding energy vs. natural compounds (curcumin) using molecular dynamics of force fields CHARMM." In THE 3RD INTERNATIONAL CONFERENCE ON PHYSICAL INSTRUMENTATION AND ADVANCED MATERIALS (ICPIAM) 2021. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0108013.

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MAGNIN, J., E. CUAUTLE, G. HERRERA, and A. SÁNCHEZ-HERNÁNDEZ. "CHARGE ASYMMETRIES IN CHARM PHOTO-PRODUCTION." In Proceedings of the VIII International Workshop. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704429_0039.

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Lynch, Alec, Marjorie Shapiro, and Miha Muskinja. "W+D Charm Jet Fragmentation." In W+D Charm Jet Fragmentation. US DOE, 2024. http://dx.doi.org/10.2172/2406067.

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DUNNE, WILLIAM. "CHARMED-HADRON PRODUCTION AND CHARM FRAGMENTATION AT ZEUS." In Proceedings of the 14th International Workshop. WORLD SCIENTIFIC, 2007. http://dx.doi.org/10.1142/9789812706706_0133.

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Scomparin, Enrico. "Charmonium physics with heavy ions: experimental results." In VIII International Workshop On Charm Physics. Sissa Medialab, 2017. http://dx.doi.org/10.22323/1.289.0008.

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Vairo, Antonio. "Quarkonium evolution and suppression in a strongly-coupled quark-gluon plasma." In VIII International Workshop On Charm Physics. Sissa Medialab, 2017. http://dx.doi.org/10.22323/1.289.0009.

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Reports on the topic "CHARMM"

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David A. Case, Ph D., and Ph D. Charles L. Brooks III. Biomolecular Simulation Using Amber and CHARMM. Office of Scientific and Technical Information (OSTI), 2004. http://dx.doi.org/10.2172/835140.

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Gouwy, S. A. Devonian conodont biostratigraphy of the Mackenzie Mountains, western part of the Northwest Territories. Natural Resources Canada/CMSS/Information Management, 2022. http://dx.doi.org/10.4095/326098.

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In this paper, a review of the current understanding of Devonian conodont biostratigraphy in the Mackenzie Mountains in the Northwest Territories is presented. The Devonian stratigraphy of the northern and southern Mackenzie Mountains is presented on two chronostratigraphic charts, from the first deposits on top of the sub-Devonian unconformity to the lower part of the Imperial and Fort Simpson formations. Schematic maps give an overview of the regional distribution of the formations in the Mackenzie Mountains. This update revealed that several of the assemblage and formation contacts are youn
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Shukla, S. Excited Charm States. Office of Scientific and Technical Information (OSTI), 1994. http://dx.doi.org/10.2172/10114961.

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Anjos, J. C. C., A. F. S. Santoro, M. H. G. Souza, et al. Pion and Kaon Production of Charm and Charm-Strange States. Office of Scientific and Technical Information (OSTI), 1985. http://dx.doi.org/10.2172/1000260.

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Wallace, Andrew Faulkner. Hadroproduction of Charm Mesons. Office of Scientific and Technical Information (OSTI), 1997. http://dx.doi.org/10.2172/1421724.

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Charles, M. Charm Decays at BABAR. Office of Scientific and Technical Information (OSTI), 2004. http://dx.doi.org/10.2172/839979.

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Edwards, Adam J. A Study of Double-Charm and Charm-Strange Baryons inElectron-Positron Annihilations. Office of Scientific and Technical Information (OSTI), 2007. http://dx.doi.org/10.2172/918027.

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Cinquini, Luca. Analysis of charm meson semileptonic decays and charm baryon high mass states. Office of Scientific and Technical Information (OSTI), 1995. http://dx.doi.org/10.2172/1423651.

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Wilkowski, Gery. PR-276-223814-R01 Pragmatic Application of MegaRule RIN 1 - 192.712 Toughness Values. Pipeline Research Council International, Inc. (PRCI), 2024. http://dx.doi.org/10.55274/r0000057.

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This project addresses pragmatic application of the new DOT/PHMSA MegaRule RIN 1 - 192.712 for recommended toughness values for determining if an axial flaw needs repair or can instead be observed for any future growth. The MegaRule toughness is expressed as the Charpy energy value, which came from Charpy test data at 50F. However, the fracture toughness of a surface-cracked pipe is quite different than Charpy impact toughness values, especially if the Charpy data is in the transition region. In this project, it was shown from past axial surface-cracked pipe tests that the lowest temperature f
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Travis, Amanda, Margaret Harvey, and Michelle Rickard. Adverse Childhood Experiences and Urinary Incontinence in Elementary School Aged Children. University of Tennessee Health Science Center, 2021. http://dx.doi.org/10.21007/con.dnp.2021.0012.

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Purpose/Background: Adverse Childhood Experiences (ACEs) have an impact on health throughout the lifespan (Filletti et al., 1999; Hughes et al., 2017). These experiences range from physical and mental abuse, substance abuse in the home, parental separation or loss, financial instability, acute illness or injury, witnessing violence in the home or community, and incarceration of family members (Hughes et al., 2017). Understanding and screening for ACEs in children with urinary incontinence can help practitioners identify psychological stress as a potentially modifiable risk factor. Methods: A 5
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