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Modelling of β-D-glucopyranose ring distortion in different force fields: a metadynamics study
Title Modelling of β-D-glucopyranose ring distortion in different force fields: a metadynamics study Author Spiwok Vojtech SAVCHEM - Chemický ústav SAV Tvaroška Igor 1944 SAVCHEM - Chemický ústav SAV SCOPUS RID ORCID Co-authors Králová Blanka Source document Carbohydrate Research. Vol.345, (2010), p. 530-537 Language eng - English Document kind rozpis článkov z periodík (rbx) Citations Ardevol, A (Ardevol, Albert); Biarnes, X (Biarnes, Xevi); Planas, A (Planas, Antoni); Rovira, C (Rovira, Carme) Title: The Conformational Free-Energy Landscape of beta-D-Mannopyranose: Evidence for a (1)S(5) -> B(2,5) -> (O)S(2) Catalytic Itinerary in beta-Mannosidases Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Volume: 132 Issue: 45 Pages: 16058-16065 DOI: 10.1021/ja105520h Published: NOV 17 2010 Autieri, E (Autieri, E.); Sega, M (Sega, M.); Pederiva, F (Pederiva, F.); Guella, G (Guella, G.) Title: Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation Source: JOURNAL OF CHEMICAL PHYSICS Volume: 133 Issue: 9 Article Number: 095104 DOI: 10.1063/1.3476466 Published: SEP 7 2010 Babin, V (Babin, Volodymyr); Sagui, C (Sagui, Celeste) Title: Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water Source: JOURNAL OF CHEMICAL PHYSICS Volume: 132 Issue: 10 Article Number: 104108 DOI: 10.1063/1.3355621 Published: MAR 14 2010 SATTELLE, Benedict M. - ALMOND, Andrew. Is N-acetyl-d-glucosamine a rigid C-4(1) chair? In GLYCOBIOLOGY, 2011, vol. 21, no. 12, pp. 1651-1662. ISSN 0959-6658. Dostupné na: https://doi.org/10.1093/glycob/cwr101. KUTTEL, Michelle M. The Conformational Free Energy of Carbohydrates. In MINI-REVIEWS IN ORGANIC CHEMISTRY, 2011, vol. 8, no. 3, pp. 256-262. ISSN 1570-193X. HANSEN, Halvor S. - HUENENBERGER, Philippe H. A Reoptimized GROMOS Force Field for Hexopyranose-Based Carbohydrates Accounting for the Relative Free Energies of Ring Conformers, Anomers, Epimers, Hydroxymethyl Rotamers, and Glycosidic Linkage Conformers. In JOURNAL OF COMPUTATIONAL CHEMISTRY, 2011, vol. 32, no. 6, pp. 998-1032. ISSN 0192-8651. Dostupné na: https://doi.org/10.1002/jcc.21675. ZHANG, Qiong - BULONE, Vincent - AGREN, Hans - TU, Yaoquan. A molecular dynamics study of the thermal response of crystalline cellulose I beta. In CELLULOSE, 2011, vol. 18, no. 2, pp. 207-221. ISSN 0969-0239. Dostupné na: https://doi.org/10.1007/s10570-010-9491-x. SEGA, M. - AUTIERI, E. - PEDERIVA, F. Pickett angles and Cremer-Pople coordinates as collective variables for the enhanced sampling of six-membered ring conformations. In MOLECULAR PHYSICS, 2011, vol. 109, no. 1, pp. 141-148. ISSN 0026-8976. Dostupné na: https://doi.org/10.1080/00268976.2010.522208. SAHA, Jaideep - PECZUH, Mark W. SYNTHESIS AND PROPERTIES OF SEPTANOSE CARBOHYDRATES. In ADVANCES IN CARBOHYDRATE CHEMISTRY AND BIOCHEMISTRY, VOL 66, 2011, vol. 66, no., pp. 121-186. ISSN 0065-2318. Dostupné na: https://doi.org/10.1016/B978-0-12-385518-3.00003-1. Pol-Fachin, L (Pol-Fachin, Laercio); Rusu, VH (Rusu, Victor H.); Verli, H (Verli, Hugo); Lins, RD (Lins, Roberto D.) In. JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 8 Issue: 11 Pages: 4681-4690 Islam, SM (Islam, Shahidul M.); Roy, PN (Roy, Pierre-Nicholas) In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 8 Issue: 7 Pages: 2412-2423 Sattelle, BM (Sattelle, Benedict M.); Bose-Basu, B (Bose-Basu, Bidisha); Tessier, M (Tessier, Matthew); Woods, RJ (Woods, Robert J.); Serianni, AS (Serianni, Anthony S.); Almond, A (Almond, Andrew) In: JOURNAL OF PHYSICAL CHEMISTRY B Volume: 116 Issue: 22 Pages: 6380-6386 Davies, GJ (Davies, Gideon J.); Planas, A (Planas, Antoni); Rovira, C (Rovira, Carme) In: ACCOUNTS OF CHEMICAL RESEARCH Volume: 45 Issue: 2 Pages: 308-316 French, AD (French, Alfred D.) In: ADVANCES IN CARBOHYDRATE CHEMISTRY AND BIOCHEMISTRY, VOL 67 Book Series: Advances in Carbohydrate Chemistry and Biochemistry Volume: 67 Pages: 19-93 Sattelle, BM (Sattelle, Benedict M.); Almond, A (Almond, Andrew) In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS Volume: 14 Issue: 16 Pages: 5843-5848 Matthews, JF (Matthews, James F.); Beckham, GT (Beckham, Gregg T.); Bergenstrahle-Wohlert, M (Bergenstrahle-Wohlert, Malin); Brady, JW (Brady, John W.); Himmel, ME (Himmel, Michael E.); Crowley, MF (Crowley, Michael F.) In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 8 Issue: 2 Pages: 735-748 Branduardi, D (Branduardi, Davide); Faraldo-Gomez, JD (Faraldo-Gomez, Jose D.), In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 9 Issue: 9 Pages: 4140-4154 Wolter, T (Wolter, Tino); Steinbrecher, T (Steinbrecher, Thomas); Elstner, M (Elstner, Marcus), In: PLOS ONE Volume: 8 Issue: 3 Article Number: e58774 Taha, HA (Taha, Hashem A.); Richards, MR (Richards, Michele R.); Lowary, TL (Lowary, Todd L.), In: CHEMICAL REVIEWS Volume: 113 Issue: 3 Pages: 1851-1876 Bocahut, A (Bocahut, Anthony); Delannoy, JY (Delannoy, Jean-Yves); Vergelati, C (Vergelati, Caroll); Mazeau, K (Mazeau, Karim), In: CELLULOSE Volume: 21 Issue: 6 Pages: 3897-3912 Rusu, VH (Rusu, Victor H.); Baron, R (Baron, Riccardo); Lins, RD (Lins, Roberto D.), In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 10 Issue: 11 Pages: 5068-5080 Momany, F (Momany, Frank); Schnupf, U (Schnupf, Udo), In: COMPUTATIONAL AND THEORETICAL CHEMISTRY Volume: 1029 Pages: 57-67 Plazinski, W (Plazinski, Wojciech); Drach, M (Drach, Mateusz), In: RSC ADVANCES Volume: 4 Issue: 48 Pages: 25028-25039 PLAZINSKI, Wojciech - DRACH, Mateusz. Kinetic characteristics of conformational changes in the hexopyranose rings. In CARBOHYDRATE RESEARCH. ISSN 0008-6215, 2015, vol. 416, no., pp. 41-50. PLAZINSKI, Wojciech - DRACH, Mateusz. The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations. In CARBOHYDRATE RESEARCH. ISSN 0008-6215, 2015, vol. 415, no., pp. 17-27. TANKRATHOK, Anupong - IGLESIAS-FERNANDEZ, Javier - WILLIAMS, Rohan J. - PENGTHAISONG, Salila - BAIYA, Supaporn - HAKKI, Zalihe - ROBINSON, Robert C. - HRMOVA, Maria - ROVIRA, Carme - WILLIAMS, Spencer J. - CAIRNS, James R. Ketudat. A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides. In ACS CATALYSIS. ISSN 2155-5435, 2015, vol. 5, no. 10, pp. 6041-6051. LOERBROKS, Claudia - BOULANGER, Eliot - THIEL, Walter. Solvent Influence on Cellulose 1,4-beta-Glycosidic Bond Cleavage: A Molecular Dynamics and Metadynarnics Study. In CHEMISTRY-A EUROPEAN JOURNAL. ISSN 0947-6539, 2015, vol. 21, no. 14, pp. 5477-5487. YANG, Mingjun - MACKERELL, Alexander D. Conformational Sampling of Oligosaccharides Using Hamiltonian Replica Exchange with Two-Dimensional Dihedral Biasing Potentials and the Weighted Histogram Analysis Method (WHAM). In JOURNAL OF CHEMICAL THEORY AND COMPUTATION. ISSN 1549-9618, 2015, vol. 11, no. 2, pp. 788-799. XIONG, Xiuming - CHEN, Zhaoqiang - COSSINS, Benjamin P. - XU, Zhijian - SHAO, Qiang - DING, Kai - ZHU, Weiliang - SHI, Jiye. Force fields and scoring functions for carbohydrate simulation. In CARBOHYDRATE RESEARCH. ISSN 0008-6215, 2015, vol. 401, no., pp. 73-81. IGLESIAS-FERNANDEZ, Javier - RAICH, Lluis - ARDEVOL, Albert - ROVIRA, Carme. The complete conformational free energy landscape of beta-xylose reveals a two-fold catalytic itinerary for beta-xylanases. In CHEMICAL SCIENCE. ISSN 2041-6520, 2015, vol. 6, no. 2, pp. 1167-1177. FRENCH, Alfred D. Computerized models of carbohydrates. In Polysaccharides: Bioactivity and Biotechnology, 2015-01-01, pp. 1397-1440. MARIANSKI, Mateusz - SUPADY, Adriana - INGRAM, Teresa - SCHNEIDER, Markus - BALDAUF, Carsten. Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and alpha-Maltose. In JOURNAL OF CHEMICAL THEORY AND COMPUTATION. ISSN 1549-9618, 2016, vol. 12, no. 12, pp. 6157-6168. HASHEMIAN, Behrooz - MILLAN, Daniel - ARROYO, Marino. Charting molecular free-energy landscapes with an atlas of collective variables. In JOURNAL OF CHEMICAL PHYSICS. ISSN 0021-9606, 2016, vol. 145, no. 17, pp. CORREDOR, Miriam - BONET, Roman - MOURE, Alejandra - DOMINGO, Cecilia - BUJONS, Jordi - ALFONSO, Ignacio - PEREZ, Yolanda - MESSEGUER, Angel. Cationic Peptides and Peptidomimetics Bind Glycosaminoglycans as Potential Sema3A Pathway Inhibitors. In BIOPHYSICAL JOURNAL. ISSN 0006-3495, 2016, vol. 110, no. 6, pp. 1291-1303. PLAZINSKI, Wojciech - LONARDI, Alice - HUENENBERGER, Philippe H. Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains. In JOURNAL OF COMPUTATIONAL CHEMISTRY. ISSN 0192-8651, 2016, vol. 37, no. 3, pp. 354-365. RAICH, L. - NIN-HILL, A. - ARDEVOL, A. - ROVIRA, C. Enzymatic Cleavage of Glycosidic Bonds: Strategies on How to Set Up and Control a QM/MM Metadynamics Simulation. In COMPUTATIONAL APPROACHES FOR STUDYING ENZYME MECHANISM, PT A. ISSN 0076-6879, 2016, vol. 577, no., pp. 159-183. PLAZINSKI, Wojciech - PLAZINSKA, Anita. Molecular dynamics simulations of hexopyranose ring distortion in different force fields. In PURE AND APPLIED CHEMISTRY. ISSN 0033-4545, 2017, vol. 89, no. 9, pp. 1283-1294. VICKMAN, Alison E. - ASHLEY, Daniel C. - BAIK, Mu-Hyun - POHL, Nicola L. B. Effects of varying the 6-position oxidation state of hexopyranoses: a systematic comparative computational analysis of 48 monosaccharide stereoisomers. In JOURNAL OF MOLECULAR MODELING. ISSN 1610-2940, 2017, vol. 23, no. 7, pp. JIANG, Xue-Wei - ZHANG, Hong-Hui - ZHONG, An-Hua. Analysis on Van der Waals and Electrostatic Interaction of Crystalline Cellulose I beta Based on Molecular Dynamics. In TEXTILE BIOENGINEERING AND INFORMATICS SYMPOSIUM PROCEEDINGS, 2017, VOL. 3. ISSN 1942-3438, 2017, vol., no., pp. 1260-1266. MONTGOMERY, Andrew P. - XIAO, Kela - WANG, Xingyong - SKROPETA, Danielle - YU, Haibo. Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design. In STRUCTURAL AND MECHANISTIC ENZYMOLOGY. ISSN 1876-1623, 2017, vol. 109, no., pp. 25-76. UTO, Takuya - YUI, Toshtfumi. Higher Ordered Structure of Cellulose Predicted by Computational Chemistry: Cellulose Nanotube in Cyclohexane and Ethyl Acetate. In JOURNAL OF FIBER SCIENCE AND TECHNOLOGY. ISSN 2189-7654, 2018, vol. 74, no. 8, pp. 171-176. UTO, Takuya - YAMAMOTO, Kazuya - KADOKAWA, Jun-ichi. Cellulose Crystal Dissolution in Imidazolium-Based Ionic Liquids: A Theoretical Study. In JOURNAL OF PHYSICAL CHEMISTRY B. ISSN 1520-6106, 2018, vol. 122, no. 1, pp. 258-266. PANCZYK, Karina - PLAZINSKI, Wojciech. Pyranose ring puckering in aldopentoses, ketohexoses and deoxyaldohexoses. A molecular dynamics study. In CARBOHYDRATE RESEARCH. ISSN 0008-6215, 2018, vol. 455, no., pp. 62-70. KUTTEL, Michelle M. - RAVENSCROFT, Neil. The Role of Molecular Modeling in Predicting Carbohydrate Antigen Conformation and Understanding Vaccine Immunogenicity. In CARBOHYDRATE-BASED VACCINES: FROM CONCEPT TO CLINIC. ISSN 0097-6156, 2018, vol. 1290, no., pp. 139-173. ALIBAY, Irfan - BRYCE, Richard A. Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations. In JOURNAL OF CHEMICAL INFORMATION AND MODELING. ISSN 1549-9596, 2019, vol. 59, no. 11, pp. 4729-4741. NAGARAJAN, Balaji - SANKARANARAYANAN, Nehru Viji - DESAI, Umesh R. Perspective on computational simulations of glycosaminoglycans. In WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE. ISSN 1759-0876, 2019, vol. 9, no. 2, pp. IKEJO, Makoto - WATANABE, Hirofumi - SHIMAMURA, Kohei - TANAKA, Shigenori. Improvement of the Force Field for beta-d-Glucose with Machine Learning. In MOLECULES, 2021, vol. 26, no. 21, pp. Dostupné na: https://doi.org/10.3390/molecules26216691. GESTEIRA, Tarsis Ferreira - MARFORIO, Tainah Dorina - MUELLER, Jonathan Wolf - CALVARESI, Matteo - COULSON-THOMAS, Vivien Jane. Structural Determinants of Substrate Recognition and Catalysis by Heparan Sulfate Sulfotransferases. In ACS CATALYSIS, 2021, vol. 11, no. 17, pp. 10974-10987. ISSN 2155-5435. 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Category ADCA - Scientific papers in foreign journals registered in Current Contents Connect with IF (impacted) Category of document (from 2022) V3 - Vedecký výstup publikačnej činnosti z časopisu Type of document článok Year 2010 Registered in WOS Registered in SCOPUS Registered in CCC DOI 10.1016/j.carres.2009.12.011 
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rok CC IF IF Q (best) JCR Av Jour IF Perc SJR SJR Q (best) CiteScore A rok vydania rok metriky IF IF Q (best) SJR SJR Q (best) 2010 2009 2.025 Q2 0.888 Q1
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