ACS Publications. Most Trusted. Most Cited. Most Read
My Activity
CONTENT TYPES

Figure 1Loading Img
ADDITION / CORRECTIONThis article has been corrected. View the notice.

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

  • Petra Kührová
    Petra Kührová
    Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
    Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
  • Vojtěch Mlýnský
    Vojtěch Mlýnský
    Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
  • Marie Zgarbová
    Marie Zgarbová
    Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
    Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
  • Miroslav Krepl
    Miroslav Krepl
    Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
    Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
  • Giovanni Bussi
    Giovanni Bussi
    Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
  • Robert B. Best
    Robert B. Best
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
  • Michal Otyepka
    Michal Otyepka
    Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
    Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
  • Jiří Šponer*
    Jiří Šponer
    Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
    Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
    *E-mail: [email protected]
  • , and 
  • Pavel Banáš*
    Pavel Banáš
    Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
    Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
    Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
    *E-mail: [email protected]
Cite this: J. Chem. Theory Comput. 2019, 15, 5, 3288–3305
Publication Date (Web):March 21, 2019
https://doi.org/10.1021/acs.jctc.8b00955
Copyright © 2019 American Chemical Society

    Article Views

    2817

    Altmetric

    -

    Citations

    LEARN ABOUT THESE METRICS
    Other access options
    Supporting Info (3)»

    Abstract

    Abstract Image

    Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force fields, ffs), RNA ffs have persisting deficiencies, which hamper their utilization in quantitatively accurate simulations. Previous studies have shown that at least two salient problems contribute to difficulties in the description of free-energy landscapes of small RNA motifs: (i) excessive stabilization of the unfolded single-stranded RNA ensemble by intramolecular base–phosphate and sugar–phosphate interactions and (ii) destabilization of the native folded state by underestimation of stability of base pairing. Here, we introduce a general ff term (gHBfix) that can selectively fine-tune nonbonding interaction terms in RNA ffs, in particular, the H bonds. The gHBfix potential affects the pairwise interactions between all possible pairs of the specific atom types, while all other interactions remain intact; i.e., it is not a structure-based model. In order to probe the ability of the gHBfix potential to refine the ff nonbonded terms, we performed an extensive set of folding simulations of RNA tetranucleotides and tetraloops. On the basis of these data, we propose particular gHBfix parameters to modify the AMBER RNA ff. The suggested parametrization significantly improves the agreement between experimental data and the simulation conformational ensembles, although our current ff version still remains far from being flawless. While attempts to tune the RNA ffs by conventional reparametrizations of dihedral potentials or nonbonded terms can lead to major undesired side effects, as we demonstrate for some recently published ffs, gHBfix has a clear promising potential to improve the ff performance while avoiding introduction of major new imbalances.

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Supporting Information

    ARTICLE SECTIONS
    Jump To

    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jctc.8b00955.

    • Details about convergence of enhanced-sampling simulations, description of the r(gcUUCGgc) T-REMD folding simulation with structure specific HBfix, detailed description of additional REST2 folding simulations with various gHBfix potentials, further details about the relation between the gHBfix and NBfix approaches, structure preparation and other details about simulation protocols, detailed description of REST2 and standard MD simulations with recently published ffs, description of standard MD simulations with the gHBfix potential, and Supporting Tables and Figures (PDF)

    • C++ code to generate inputs for AMBER and GROMACS in order to perform simulations with the gHBfix (PDF)

    • AMBER input files containing DESRES parameters (ZIP)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    This article is cited by 77 publications.

    1. Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiří Šponer, Petr Stadlbauer. Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of Chemical Information and Modeling 2024, Article ASAP.
    2. Taeyoung Choi, Zhengxin Li, Ge Song, Hai-Feng Chen. Comprehensive Comparison and Critical Assessment of RNA-Specific Force Fields. Journal of Chemical Theory and Computation 2024, 20 (6) , 2676-2688. https://doi.org/10.1021/acs.jctc.4c00066
    3. Lisa M. Pietrek, Lukas S. Stelzl, Gerhard Hummer. Hierarchical Assembly of Single-Stranded RNA. Journal of Chemical Theory and Computation 2024, 20 (5) , 2246-2260. https://doi.org/10.1021/acs.jctc.3c01049
    4. Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya. Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations. ACS Omega 2024, 9 (3) , 3412-3422. https://doi.org/10.1021/acsomega.3c06826
    5. Vojtěch Mlýnský, Petra Kührová, Petr Stadlbauer, Miroslav Krepl, Michal Otyepka, Pavel Banáš, Jiří Šponer. Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations. Journal of Chemical Theory and Computation 2023, 19 (22) , 8423-8433. https://doi.org/10.1021/acs.jctc.3c00990
    6. Sunil Kumar, Govardhan Reddy. Mechanism of Fluoride Ion Encapsulation by Magnesium Ions in a Bacterial Riboswitch. The Journal of Physical Chemistry B 2023, 127 (43) , 9267-9281. https://doi.org/10.1021/acs.jpcb.3c03941
    7. Rafael G. Viegas, Murilo N. Sanches, Alan A. Chen, Fernando V. Paulovich, Angel E. Garcia, Vitor B. P. Leite. Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop. Journal of Chemical Information and Modeling 2023, 63 (17) , 5641-5649. https://doi.org/10.1021/acs.jcim.3c00426
    8. Petr Stadlbauer, Vojtěch Mlýnský, Miroslav Krepl, Jiří Šponer. Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. Journal of Chemical Information and Modeling 2023, 63 (15) , 4716-4731. https://doi.org/10.1021/acs.jcim.3c00171
    9. Benedetta Petra Rosi, Valeria Libera, Luca Bertini, Andrea Orecchini, Silvia Corezzi, Giorgio Schirò, Petra Pernot, Ralf Biehl, Caterina Petrillo, Lucia Comez, Cristiano De Michele, Alessandro Paciaroni. Stacking Interactions and Flexibility of Human Telomeric Multimers. Journal of the American Chemical Society 2023, 145 (29) , 16166-16175. https://doi.org/10.1021/jacs.3c04810
    10. Kosar Rahimi, Pablo M. Piaggi, Gül H. Zerze. Comparison of On-the-Fly Probability Enhanced Sampling and Parallel Tempering Combined with Metadynamics for Atomistic Simulations of RNA Tetraloop Folding. The Journal of Physical Chemistry B 2023, 127 (21) , 4722-4732. https://doi.org/10.1021/acs.jpcb.3c00117
    11. Zhengyue Zhang, Jiří Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Šulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl. Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of Chemical Information and Modeling 2023, 63 (9) , 2794-2809. https://doi.org/10.1021/acs.jcim.3c00358
    12. Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiří Šponer, Pavel Banáš. Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. Journal of Chemical Information and Modeling 2023, 63 (7) , 2133-2146. https://doi.org/10.1021/acs.jcim.2c01438
    13. Klaudia Mráziková, Holger Kruse, Vojtěch Mlýnský, Pascal Auffinger, Jiří Šponer. Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. Journal of Chemical Information and Modeling 2022, 62 (23) , 6182-6200. https://doi.org/10.1021/acs.jcim.2c01064
    14. Pavlína Pokorná, Miroslav Krepl, Sébastien Campagne, Jiří Šponer. Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations. The Journal of Physical Chemistry B 2022, 126 (45) , 9207-9221. https://doi.org/10.1021/acs.jpcb.2c06168
    15. Zhifeng Jing, Pengyu Ren. Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model. The Journal of Physical Chemistry B 2022, 126 (38) , 7343-7353. https://doi.org/10.1021/acs.jpcb.2c05278
    16. Valerio Piomponi, Thorben Fröhlking, Mattia Bernetti, Giovanni Bussi. Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine. ACS Central Science 2022, 8 (8) , 1218-1228. https://doi.org/10.1021/acscentsci.2c00565
    17. Thorben Fröhlking, Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Miroslav Krepl, Pavel Banáš, Jiří Šponer, Giovanni Bussi. Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. Journal of Chemical Theory and Computation 2022, 18 (7) , 4490-4502. https://doi.org/10.1021/acs.jctc.2c00200
    18. Maxwell R. Tucker, Stefano Piana, Dazhi Tan, Michael V. LeVine, David E. Shaw. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA–Protein Complexes. The Journal of Physical Chemistry B 2022, 126 (24) , 4442-4457. https://doi.org/10.1021/acs.jpcb.1c10971
    19. Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Thorben Fröhlking, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiří Šponer. Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications. Journal of Chemical Theory and Computation 2022, 18 (4) , 2642-2656. https://doi.org/10.1021/acs.jctc.1c01222
    20. Jianbo Zhao, Scott D. Kennedy, Douglas H. Turner. Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA. Journal of Chemical Theory and Computation 2022, 18 (2) , 1241-1254. https://doi.org/10.1021/acs.jctc.1c00643
    21. Gül H. Zerze, Pablo M. Piaggi, Pablo G. Debenedetti. A Computational Study of RNA Tetraloop Thermodynamics, Including Misfolded States. The Journal of Physical Chemistry B 2021, 125 (50) , 13685-13695. https://doi.org/10.1021/acs.jpcb.1c08038
    22. Klaudia Mráziková, Jiří Šponer, Vojtěch Mlýnský, Pascal Auffinger, Holger Kruse. Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids. Journal of Chemical Information and Modeling 2021, 61 (11) , 5644-5657. https://doi.org/10.1021/acs.jcim.1c01047
    23. Miroslav Krepl, Fred Franz Damberger, Christine von Schroetter, Dominik Theler, Pavlína Pokorná, Frédéric H.-T. Allain, Jiří Šponer. Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration. The Journal of Physical Chemistry B 2021, 125 (28) , 7691-7705. https://doi.org/10.1021/acs.jpcb.1c03541
    24. Zhixiong Lin, Junjie Zou, Shuai Liu, Chunwang Peng, Zhipeng Li, Xiao Wan, Dong Fang, Jian Yin, Gianpaolo Gobbo, Yongpan Chen, Jian Ma, Shuhao Wen, Peiyu Zhang, Mingjun Yang. A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Predictions: New Opportunities and Challenges for Drug Discovery. Journal of Chemical Information and Modeling 2021, 61 (6) , 2720-2732. https://doi.org/10.1021/acs.jcim.0c01329
    25. Michal Janeček, Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiří Šponer, Pavel Banáš. W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model. Journal of Chemical Theory and Computation 2021, 17 (6) , 3495-3509. https://doi.org/10.1021/acs.jctc.0c00976
    26. Lev Levintov, Sanjib Paul, Harish Vashisth. Reaction Coordinate and Thermodynamics of Base Flipping in RNA. Journal of Chemical Theory and Computation 2021, 17 (3) , 1914-1921. https://doi.org/10.1021/acs.jctc.0c01199
    27. Klaudia Mráziková, Vojtěch Mlýnský, Petra Kührová, Pavlína Pokorná, Holger Kruse, Miroslav Krepl, Michal Otyepka, Pavel Banáš, Jiří Šponer. UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations. Journal of Chemical Theory and Computation 2020, 16 (12) , 7601-7617. https://doi.org/10.1021/acs.jctc.0c00801
    28. Antarip Halder, Sunil Kumar, Omar Valsson, Govardhan Reddy. Mg2+ Sensing by an RNA Fragment: Role of Mg2+-Coordinated Water Molecules. Journal of Chemical Theory and Computation 2020, 16 (10) , 6702-6715. https://doi.org/10.1021/acs.jctc.0c00589
    29. Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai. Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters. Journal of Chemical Theory and Computation 2020, 16 (9) , 5923-5935. https://doi.org/10.1021/acs.jctc.0c00270
    30. Vojtěch Mlýnský, Petra Kührová, Tomáš Kühr, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiří Šponer. Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. Journal of Chemical Theory and Computation 2020, 16 (6) , 3936-3946. https://doi.org/10.1021/acs.jctc.0c00228
    31. Barira Islam, Petr Stadlbauer, Michaela Vorlíčková, Jean-Louis Mergny, Michal Otyepka, Jiří Šponer. Stability of Two-Quartet G-Quadruplexes and Their Dimers in Atomistic Simulations. Journal of Chemical Theory and Computation 2020, 16 (6) , 3447-3463. https://doi.org/10.1021/acs.jctc.9b01068
    32. Evangelia Pantatosaki, George K. Papadopoulos. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides’ Functional Groups and Stereoisomerism. Journal of Chemical Theory and Computation 2020, 16 (6) , 3842-3855. https://doi.org/10.1021/acs.jctc.9b01261
    33. Jianbo Zhao, Scott D. Kennedy, Kyle D. Berger, Douglas H. Turner. Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2020, 16 (3) , 1968-1984. https://doi.org/10.1021/acs.jctc.9b00912
    34. Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B. Best, Michal Otyepka, Jiří Šponer, Pavel Banáš. Correction to “Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions”. Journal of Chemical Theory and Computation 2020, 16 (1) , 818-819. https://doi.org/10.1021/acs.jctc.9b01189
    35. Yaozong Li, Rajiv Kumar Bedi, Lars Wiedmer, Danzhi Huang, Paweł Śledź, Amedeo Caflisch. Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif. Journal of Chemical Theory and Computation 2019, 15 (12) , 7004-7014. https://doi.org/10.1021/acs.jctc.9b00987
    36. Zhifeng Jing, Rui Qi, Marc Thibonnier, Pengyu Ren. Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. Journal of Chemical Theory and Computation 2019, 15 (11) , 6422-6432. https://doi.org/10.1021/acs.jctc.9b00519
    37. Pavlína Pokorná, Miroslav Krepl, Eva Bártová, Jiří Šponer. Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network. Journal of Chemical Theory and Computation 2019, 15 (10) , 5659-5673. https://doi.org/10.1021/acs.jctc.9b00434
    38. R. G. Efremov. Dielectric-Dependent Strength of Interlipid Hydrogen Bonding in Biomembranes: Model Case Study. Journal of Chemical Information and Modeling 2019, 59 (6) , 2765-2775. https://doi.org/10.1021/acs.jcim.9b00193
    39. Andrea Cesari, Sandro Bottaro, Kresten Lindorff-Larsen, Pavel Banáš, Jiří Šponer, Giovanni Bussi. Fitting Corrections to an RNA Force Field Using Experimental Data. Journal of Chemical Theory and Computation 2019, 15 (6) , 3425-3431. https://doi.org/10.1021/acs.jctc.9b00206
    40. Raju Sarkar, Avijit Mainan, Susmita Roy. Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods. Chemical Communications 2024, 60 (27) , 3624-3644. https://doi.org/10.1039/D3CC06105A
    41. Pavlína Pokorná, Vojtěch Mlýnský, Giovanni Bussi, Jiří Šponer, Petr Stadlbauer. Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble. International Journal of Biological Macromolecules 2024, 261 , 129712. https://doi.org/10.1016/j.ijbiomac.2024.129712
    42. Korbinian Liebl, Martin Zacharias. The development of nucleic acids force fields: From an unchallenged past to a competitive future. Biophysical Journal 2023, 122 (14) , 2841-2851. https://doi.org/10.1016/j.bpj.2022.12.022
    43. Jure Borišek, Jana Aupič, Alessandra Magistrato. Establishing the catalytic and regulatory mechanism of RNA ‐based machineries. WIREs Computational Molecular Science 2023, 13 (3) https://doi.org/10.1002/wcms.1643
    44. Fai-Chu Wong, You-Han Lee, Joe-Hui Ong, Fazilah Abd Manan, Mohamad Zulkeflee Sabri, Tsun-Thai Chai. Exploring the Potential of Black Soldier Fly Larval Proteins as Bioactive Peptide Sources through in Silico Gastrointestinal Proteolysis: A Cheminformatic Investigation. Catalysts 2023, 13 (3) , 605. https://doi.org/10.3390/catal13030605
    45. Wojciech K. Kasprzak, Bruce A. Shapiro. Application of Molecular Dynamics to Expand Docking Program’s Exploratory Capabilities and to Evaluate Its Predictions. 2023, 75-101. https://doi.org/10.1007/978-1-0716-2687-0_6
    46. Markéta Paloncýová, Martin Pykal, Petra Kührová, Pavel Banáš, Jiří Šponer, Michal Otyepka. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. Small 2022, 18 (49) https://doi.org/10.1002/smll.202204408
    47. Zhengxin Li, Junxi Mu, Jun Chen, Hai-Feng Chen. Base-specific RNA force field improving the dynamics conformation of nucleotide. International Journal of Biological Macromolecules 2022, 222 , 680-690. https://doi.org/10.1016/j.ijbiomac.2022.09.183
    48. Miroslav Krepl, Pavlína Pokorná, Vojtěch Mlýnský, Petr Stadlbauer, Jiří Šponer. Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field. Nucleic Acids Research 2022, 50 (21) , 12480-12496. https://doi.org/10.1093/nar/gkac1106
    49. Craig L. Zirbel, Pascal Auffinger. Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey. Molecules 2022, 27 (14) , 4365. https://doi.org/10.3390/molecules27144365
    50. Yuanzhe Zhou, Yangwei Jiang, Shi‐Jie Chen. RNA –ligand molecular docking: Advances and challenges. WIREs Computational Molecular Science 2022, 12 (3) https://doi.org/10.1002/wcms.1571
    51. Weiwei He, Anja Henning-Knechtel, Serdal Kirmizialtin. Visualizing RNA Structures by SAXS-Driven MD Simulations. Frontiers in Bioinformatics 2022, 2 https://doi.org/10.3389/fbinf.2022.781949
    52. Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono, . Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex. PLOS Computational Biology 2022, 18 (1) , e1009804. https://doi.org/10.1371/journal.pcbi.1009804
    53. Jinan Wang, Lan Lan, Xiaoqing Wu, Liang Xu, Yinglong Miao. Mechanism of RNA recognition by a Musashi RNA-binding protein. Current Research in Structural Biology 2022, 4 , 10-20. https://doi.org/10.1016/j.crstbi.2021.12.002
    54. Alexandr Nasedkin, Inna Ermilova, Jan Swenson. Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule. European Biophysics Journal 2021, 50 (7) , 927-940. https://doi.org/10.1007/s00249-021-01553-1
    55. Jakob Steuer, Oleksandra Kukharenko, Kai Riedmiller, Jörg S Hartig, Christine Peter. Guanidine-II aptamer conformations and ligand binding modes through the lens of molecular simulation. Nucleic Acids Research 2021, 49 (14) , 7954-7965. https://doi.org/10.1093/nar/gkab592
    56. Iva Kejnovská, Petr Stadlbauer, Lukáš Trantírek, Daniel Renčiuk, Martin Gajarský, Daniel Krafčík, Jan Palacký, Klára Bednářová, Jiří Šponer, Jean‐Louis Mergny, Michaela Vorlíčková. G‐Quadruplex Formation by DNA Sequences Deficient in Guanines: Two Tetrad Parallel Quadruplexes Do Not Fold Intramolecularly. Chemistry – A European Journal 2021, 27 (47) , 12115-12125. https://doi.org/10.1002/chem.202100895
    57. Amal Das, Pranay Sharma, Antonio Frontera, Miquel Barcelo-Oliver, Akalesh K. Verma, Ruksana Sultana Ahmed, Sahid Hussain, Manjit K. Bhattacharyya. Supramolecular assemblies involving biologically relevant antiparallel π-stacking and unconventional solvent driven structural topology in maleato and fumarato bridged Zn( ii ) coordination polymers: antiproliferative evaluation and theoretical studies. New Journal of Chemistry 2021, 45 (29) , 13040-13055. https://doi.org/10.1039/D1NJ00619C
    58. Daria V. Berdnikova, Paolo Carloni, Sybille Krauß, Giulia Rossetti. Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding. Molecules 2021, 26 (11) , 3384. https://doi.org/10.3390/molecules26113384
    59. Yongna Yuan, Matthew J. L. Mills, Zhuangzhuang Zhang, Yan Ma, Chunyan Zhao, Wei Su. A general RNA force field: comprehensive analysis of energy minima of molecular fragments of RNA. Journal of Molecular Modeling 2021, 27 (5) https://doi.org/10.1007/s00894-021-04746-9
    60. Natacha Gillet, Alessio Bartocci, Elise Dumont. Assessing the sequence dependence of pyrimidine–pyrimidone (6–4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation. The Journal of Chemical Physics 2021, 154 (13) https://doi.org/10.1063/5.0041332
    61. Alexa M Salsbury, Justin A Lemkul. Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics. Current Opinion in Structural Biology 2021, 67 , 9-17. https://doi.org/10.1016/j.sbi.2020.08.003
    62. Nicholas Stephanopoulos, Petr Šulc. DNA Nanodevices as Mechanical Probes of Protein Structure and Function. Applied Sciences 2021, 11 (6) , 2802. https://doi.org/10.3390/app11062802
    63. Martina Lenarčič Živković, Martin Gajarský, Kateřina Beková, Petr Stadlbauer, Lukáš Vicherek, Magdalena Petrová, Radovan Fiala, Ivan Rosenberg, Jiří Šponer, Janez Plavec, Lukáš Trantírek. Insight into formation propensity of pseudocircular DNA G-hairpins. Nucleic Acids Research 2021, 49 (4) , 2317-2332. https://doi.org/10.1093/nar/gkab029
    64. Prashasti Kumar, Pratul K. Agarwal, Matthew J. Cuneo. On the Case of the Misplaced Hydrogens. ChemBioChem 2021, 22 (2) , 288-297. https://doi.org/10.1002/cbic.202000376
    65. Pavlína Pokorná, Miroslav Krepl, Jiří Šponer. Residues flanking the ARKme3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) - General Subjects 2021, 1865 (1) , 129771. https://doi.org/10.1016/j.bbagen.2020.129771
    66. Miroslav Krepl, Tom Dendooven, Ben F. Luisi, Jiri Sponer. MD simulations reveal the basis for dynamic assembly of Hfq–RNA complexes. Journal of Biological Chemistry 2021, 296 , 100656. https://doi.org/10.1016/j.jbc.2021.100656
    67. Jejoong Yoo, David Winogradoff, Aleksei Aksimentiev. Molecular dynamics simulations of DNA–DNA and DNA–protein interactions. Current Opinion in Structural Biology 2020, 64 , 88-96. https://doi.org/10.1016/j.sbi.2020.06.007
    68. Qiangqiang Duan, Peng Tao, Jun Wang, Yi Xiao. Molecular dynamics study of ways of RNA base-pair formation. Physical Review E 2020, 102 (3) https://doi.org/10.1103/PhysRevE.102.032403
    69. Hyeonjun Kim, Youngshang Pak. Balancing All‐Atom Force Field for DNA Simulations Using Osmotic Pressure Data. Bulletin of the Korean Chemical Society 2020, 41 (7) , 759-764. https://doi.org/10.1002/bkcs.12065
    70. Oscar Palomino‐Hernandez, Michael A. Margreiter, Giulia Rossetti. Challenges in RNA Regulation in Huntington's Disease: Insights from Computational Studies. Israel Journal of Chemistry 2020, 60 (7) , 681-693. https://doi.org/10.1002/ijch.202000021
    71. Thorben Fröhlking, Mattia Bernetti, Nicola Calonaci, Giovanni Bussi. Toward empirical force fields that match experimental observables. The Journal of Chemical Physics 2020, 152 (23) https://doi.org/10.1063/5.0011346
    72. Sabine Reißer, Silvia Zucchelli, Stefano Gustincich, Giovanni Bussi. Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data. Nucleic Acids Research 2020, 48 (3) , 1164-1174. https://doi.org/10.1093/nar/gkz1184
    73. Jiří Šponer, Barira Islam, Petr Stadlbauer, Shozeb Haider. Molecular dynamics simulations of G-quadruplexes: The basic principles and their application to folding and ligand binding. 2020, 197-241. https://doi.org/10.1016/bs.armc.2020.04.002
    74. Simone Orioli, Andreas Haahr Larsen, Sandro Bottaro, Kresten Lindorff-Larsen. How to learn from inconsistencies: Integrating molecular simulations with experimental data. 2020, 123-176. https://doi.org/10.1016/bs.pmbts.2019.12.006
    75. Lyudmila Dimitrova-Paternoga, Pravin Kumar Ankush Jagtap, Po-Chia Chen, Janosch Hennig. Integrative Structural Biology of Protein-RNA Complexes. Structure 2020, 28 (1) , 6-28. https://doi.org/10.1016/j.str.2019.11.017
    76. Petr Stadlbauer, Petra Kührová, Lukáš Vicherek, Pavel Banáš, Michal Otyepka, Lukáš Trantírek, Jiří Šponer. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. Nucleic Acids Research 2019, 47 (14) , 7276-7293. https://doi.org/10.1093/nar/gkz610
    77. Giovanni Pinamonti, Fabian Paul, Frank Noé, Alex Rodriguez, Giovanni Bussi. The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. The Journal of Chemical Physics 2019, 150 (15) https://doi.org/10.1063/1.5083227

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect