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Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
Title Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap Author Spiwok Vojtech SAVCHEM - Chemický ústav SAV Co-authors Králová Blanka Source document Journal of Chemical Physics. Vol. 135, (2011), p. 224504-224509 Language slo - Slovak Document kind rozpis článkov z periodík (rbx) Citations Sutto, L (Sutto, Ludovico); Marsili, S (Marsili, Simone); Gervasio, FL (Luigi Gervasio, Francesco) In: WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE Volume: 2 Issue: 5 Pages: 771-779 Tribello, GA (Tribello, Gareth A.); Ceriotti, M (Ceriotti, Michele); Parrinello, M (Parrinello, Michele) In: : PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 109 Issue: 14 Pages: 5196-5201 Thomas, PS (Thomas, Phillip S.); Somers, MF (Somers, Mark F.); Hoekstra, AW (Hoekstra, Anne W.); Kroes, GJ (Kroes, Geert-Jan) In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS Volume: 14 Issue: 24 Pages: 8628-8643 Hashemian, B (Hashemian, Behrooz); Millan, D (Millan, Daniel); Arroyo, M (Arroyo, Marino), In: JOURNAL OF CHEMICAL PHYSICS Volume: 139 Issue: 21 Article Number: 214101 Duan, MJ (Duan, Mojie); Fan, J (Fan, Jue); Li, MH (Li, Minghai); Han, L (Han, Li); Huo, SH (Huo, Shuanghong), In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 9 Issue: 5 Pages: 2490-2497 Ceriotti, M (Ceriotti, Michele); Tribello, GA (Tribello, Gareth A.); Parrinello, M (Parrinello, Michele), In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 9 Issue: 3 Pages: 1521-1532 Tribello, GA (Tribello, Gareth A.); Bonomi, M (Bonomi, Massimiliano); Branduardi, D (Branduardi, Davide); Camilloni, C (Camilloni, Carlo); Bussi, G (Bussi, Giovanni), In: COMPUTER PHYSICS COMMUNICATIONS Volume: 185 Issue: 2 Pages: 604-613 Abrams, C., & Bussi, G. , In: Entropy, 16(1), 163-199 Giorgino, T. , In: Computer Physics Communications, 185(3), 1109-1114 PFAENDTNER, Jim - BONOMI, Massimiliano. Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics. In JOURNAL OF CHEMICAL THEORY AND COMPUTATION. ISSN 1549-9618, 2015, vol. 11, no. 11, pp. 5062-5067. HASHEMIAN, Behrooz - ARROYO, Marino. Topological obstructions in the way of data-driven collective variables. In JOURNAL OF CHEMICAL PHYSICS. ISSN 0021-9606, 2015, vol. 142, no. 4, pp. DELEMOTTE, Lucie - KASIMOVA, Marina A. - KLEIN, Michael L. - TAREK, Mounir - CARNEVALE, Vincenzo. Free-energy landscape of ion-channel voltage-sensor-domain activation. In PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. ISSN 0027-8424, 2015, vol. 112, no. 1, pp. 124-129. BUSSI, Giovanni - BRANDUARDI, Davide. Free-Energy Calculations with Metadynamics: Theory and Practice. In REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28. ISSN 1069-3599, 2015, vol. 28, no., pp. 1-49. FERRAROTTI, Marco Jacopo - BOTTARO, Sandro - PEREZ-VILLA, Andrea - BUSSI, Giovanni. 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ISSN 1549-9618, 2017, vol. 13, no. 6, pp. 2489-2500. XIE, Tian - GROSSMAN, Jeffrey C. Hierarchical visualization of materials space with graph convolutional neural networks. In JOURNAL OF CHEMICAL PHYSICS. ISSN 0021-9606, 2018, vol. 149, no. 17, pp. SEO, Bumjoon - KIM, Seulwoo - LEE, Minhwan - LEE, Youn-Woo - LEE, Won Bo. Driving Conformational Transitions in the Feature Space of Autoencoder Neural Network. In JOURNAL OF PHYSICAL CHEMISTRY C. ISSN 1932-7447, 2018, vol. 122, no. 40, pp. 23224-23229. CHEN, Wei - FERGUSON, Andrew L. Molecular Enhanced Sampling with Autoencoders: On-The-Fly Collective Variable Discovery and Accelerated Free Energy Landscape Exploration. In JOURNAL OF COMPUTATIONAL CHEMISTRY. ISSN 0192-8651, 2018, vol. 39, no. 25, pp. 2079-2102. CHEN, Wei - TAN, Aik Rui - FERGUSON, Andrew L. Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design. In JOURNAL OF CHEMICAL PHYSICS. 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Curvature as a Collective Coordinate in Enhanced Sampling Membrane Simulations. In JOURNAL OF CHEMICAL THEORY AND COMPUTATION. ISSN 1549-9618, 2019, vol. 15, no. 12, pp. 6551-6561. TRIBELLO, Gareth A. - GASPAROTTO, Piero. Using Dimensionality Reduction to Analyze Protein Trajectories. In FRONTIERS IN MOLECULAR BIOSCIENCES, 2019, vol. 6, no., pp. ZHANG, ChuanBiao - YE, FangFu - LI, Ming - ZHOU, Xin. Enhanced sampling based on slow variables of trajectory mapping. In SCIENCE CHINA-PHYSICS MECHANICS & ASTRONOMY. ISSN 1674-7348, 2019, vol. 62, no. 6, pp. CERIOTTI, Michele. Unsupervised machine learning in atomistic simulations, between predictions and understanding. In JOURNAL OF CHEMICAL PHYSICS. ISSN 0021-9606, 2019, vol. 150, no. 15, pp. TRIBELLO, Gareth A. - GASPAROTTO, Piero. Using Data-Reduction Techniques to Analyze Biomolecular Trajectories. In BIOMOLECULAR SIMULATIONS: METHODS AND PROTOCOLS. ISSN 1064-3745, 2019, vol. 2022, no., pp. 453-502. BUSSI, Giovanni - TRIBELLO, Gareth A. Analyzing and Biasing Simulations with PLUMED. In BIOMOLECULAR SIMULATIONS: METHODS AND PROTOCOLS. ISSN 1064-3745, 2019, vol. 2022, no., pp. 529-578. SCHUETZ, Doris A. - BERNETTI, Mattia - BERTAZZO, Martina - MUSIL, Djordje - EGGENWEILER, Hans-Michael - RECANATINI, Maurizio - MASETTI, Matteo - ECKER, Gerhard F. - CAVALLI, Andrea. Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics. In JOURNAL OF CHEMICAL INFORMATION AND MODELING. ISSN 1549-9596, 2019, vol. 59, no. 1, pp. 535-549. BUSSI, G. - LAIO, A. Using metadynamics to explore complex free-energy landscapes. In NATURE REVIEWS PHYSICS. APR 2020, vol. 2, no. 4, p. 200-212. Dostupné na: https://doi.org/10.1038/s42254-020-0153-0. FABRIZIO, A. - MEYER, B. - CORMINBOEUF, C. Machine learning models of the energy curvature vs particle number for optimal tuning of long-range corrected functionals. In JOURNAL OF CHEMICAL PHYSICS. ISSN 0021-9606, APR 21 2020, vol. 152, no. 15. 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ISSN 0009-2665, AUG 25 2021, vol. 121, no. 16, p. 9722-9758. Dostupné na: https://doi.org/10.1021/acs.chemrev.0c01195. MUSIL, F. - GRISAFI, A. - BARTOK, A.P. - ORTNER, C. - CSANYI, G. - CERIOTTI, M. Physics-Inspired Structural Representations for Molecules and Materials. In CHEMICAL REVIEWS. ISSN 0009-2665, AUG 25 2021, vol. 121, no. 16, p. 9759-9815. Dostupné na: https://doi.org/10.1021/acs.chemrev.1c00021. 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 2011 Registered in WOS Registered in SCOPUS Registered in CCC DOI 10.1063/1.3660208 
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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) 2011 2010 2.921 Q1 1.777 Q1
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