Search results
- 1.0583260 - BFÚ 2024 RIV US eng J - Journal Article
Mlýnský, Vojtech - Kührová, Petra - Stadlbauer, Petr - Krepl, Miroslav - Otyepka, M. - Banáš, Pavel - Šponer, Jiří
Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.
Journal of Chemical Theory and Computation. Roč. 19, č. 22 (2023), s. 8423-8433. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA23-05639S
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * replica exchange * parameters * tetraloops * uucg * nmr * resolution
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 5.5, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jctc.3c00990
Permanent Link: https://hdl.handle.net/11104/0351262 - 2.0581632 - ÚFCH JH 2025 RIV US eng J - Journal Article
Saija, Maria Chiara - Vazdar, Katarina - Pajerski, Wojciech - Olžyńska, Agnieszka - Daull, P. - Garrigues, J. - Cwiklik, Lukasz
Comparative Study of Latanoprost Drug Delivery Systems for Glaucoma Treatment and Their Interaction with the Tear Film Lipid Layer Models.
Molecular Pharmaceutics. Roč. 21, č. 1 (2024), s. 126-136. ISSN 1543-8384. E-ISSN 1543-8392
R&D Projects: GA ČR(CZ) GA21-19854S
Institutional support: RVO:61388955
Keywords : bak-preserved latanoprost * pharmacokinetics * thickness * ester * oil-in-water nanoemulsion * drug delivery systems * ocular drug delivery * ophthalmology * drug formulations * latanoprost * Xalatan * Monoprost * nanomedicine * molecular dynamics simulations * Langmuir lipid films * surface tension
OECD category: Physical chemistry
Impact factor: 4.9, year: 2022
Method of publishing: Limited access
Permanent Link: https://hdl.handle.net/11104/0349741File Download Size Commentary Version Access 0581632.pdf 0 4.8 MB Publisher’s postprint require - 3.0578423 - ÚFCH JH 2025 RIV GB eng J - Journal Article
Das, D. - Bharadwaz, Priyam - Mattaparthi, V. S. K.
Computational investigation on the effect of the peptidomimetic inhibitors (NPT100-18A and NPT200-11) on the α-synuclein and lipid membrane interactions.
Journal of Biomolecular Structure & Dynamics. (2023). ISSN 0739-1102
Institutional support: RVO:61388955
Keywords : molecular-dynamics simulations * lewy body disease * parkinsons-disease * force-field * basis-sets * system * oligomerization * accumulation * mutations * mechanism * alpha-Synuclein aggregation * membrane dynamics * dft * npt100-18a * npt200-11
OECD category: Physical chemistry
Impact factor: 4.4, year: 2022
Method of publishing: Limited access
https://www.tandfonline.com/doi/abs/10.1080/07391102.2023.2262599
Permanent Link: https://hdl.handle.net/11104/0347420 - 4.0578063 - ÚFP 2024 RIV US eng J - Journal Article
Xu, Shaofeng - Jirásek, Vít - Lukeš, Petr
Elucidation of Molecular-level Mechanisms of Oxygen Atom Reactions with Chlorine Ion in NaCl Solutions using Molecular Dynamics Simulations Combined with Density Functional Theory.
ChemistrySelect. Roč. 8, č. 23 (2023), č. článku e202203937. ISSN 2365-6549. E-ISSN 2365-6549
R&D Projects: GA ČR(CZ) GA19-25026S
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61389021
Keywords : Atomic oxygen * Charge transfer * Density functional theory * Molecular dynamics simulations * NaCl
OECD category: Fluids and plasma physics (including surface physics)
Impact factor: 2.1, year: 2022
Method of publishing: Limited access
https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/slct.202203937
Permanent Link: https://hdl.handle.net/11104/0347088 - 5.0575796 - ÚT 2024 RIV US eng J - Journal Article
Klíma, M. - Celný, David - Janek, J. - Kolafa, J.
Properties of water and argon clusters developed in supersonic expansions.
Journal of Chemical Physics. Roč. 159, č. 12 (2023), č. článku 124302. ISSN 0021-9606. E-ISSN 1089-7690
R&D Projects: GA ČR(CZ) GA22-28869S
Grant - others:NVIDIA Corporation(US) A2_FCHI_2022_017
Institutional support: RVO:61388998
Keywords : molecular-dynamics simulations * supercritical solutions ress * homogeneous nucleation * rapid expansion * particle formation
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 4.4, year: 2022
Method of publishing: Open access
https://pubs.aip.org/aip/jcp/article/159/12/124302/2912115/Properties-of-water-and-argon-clusters-developed
Permanent Link: https://hdl.handle.net/11104/0347807 - 6.0575757 - ÚOCHB 2024 RIV US eng J - Journal Article
Javanainen, Matti - Heftberger, P. - Madsen, J. J. - Miettinen, M. S. - Pabst, G. - Ollila, O. H. S.
Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC-Cholesterol Interactions.
Journal of Chemical Theory and Computation. Roč. 19, č. 18 (2023), s. 6342-6352. ISSN 1549-9618. E-ISSN 1549-9626
Institutional support: RVO:61388963
Keywords : molecular-dynamics simulations * lipid-bilayer structure * small-angle neutron
OECD category: Physical chemistry
Impact factor: 5.5, year: 2022
Method of publishing: Open access
https://doi.org/10.1021/acs.jctc.3c00648
Permanent Link: https://hdl.handle.net/11104/0345487 - 7.0574950 - BFÚ 2024 RIV US eng J - Journal Article
Qiu, D. - Cheng, M. - Stadlbauer, Petr - Chen, J. - Langer, M. - Zhang, X. - Gao, Q. - Ju, H. - Šponer, Jiří - Mergny, Jean-Louis - Monchaud, D. - Zhou, J.
Topology of DNA G-Quadruplexes Can Be Harnessed in Holliday Junction-Based DNA Suprastructures to Control and Optimize Their Biocatalytic Properties.
ACS Catalysis. Roč. 13, č. 16 (2023), s. 10722-10733. ISSN 2155-5435. E-ISSN 2155-5435
R&D Projects: GA MŠMT EF15_003/0000477; GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : G-quadruplex * DNAzyme * Holliday junction * molecular dynamics simulations * catalytic mechanism
OECD category: Physical chemistry
Impact factor: 12.9, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acscatal.3c02818
Permanent Link: https://hdl.handle.net/11104/0349523 - 8.0574796 - ÚOCHB 2024 RIV GB eng J - Journal Article
Maltarollo, V. G. - da Silva, E. B. - Kronenberger, T. - Andrade, M. M. S. - de Lima Marques, G. V. - Oliveira, N. J. C. - Santos, L. H. - de Oliveira Rezende Júnior, C. - Martinho, A. C. C. - Skinner, D. - Fajtová, Pavla - Fernandes, T. H. M. - da Silveira dos Santos, E. - Gazolla, P. A. R. - de Souza, A. P. M. - da Silva, M. L. - dos Santos, F. S. - Lavorato, S. N. - Bretas, A. C. O. - Carvalho, D. T. - Franco, L. L. - Luedtke, S. - Giardini, M. A. - Poso, A. - Dias, L. C. - Podust, L. M. - Alves, R. J. - McKerrow, J. - Andrade, S. F. - Teixeira, R. R. - Siqueira-Neto, J. L. - O'Donoghue, A. - de Oliveira, R. B. - Ferreira, R. S.
Structure-based discovery of thiosemicarbazones as SARS-CoV-2 main protease inhibitors.
Future Medicinal Chemistry. Roč. 15, č. 11 (2023), s. 959-985. ISSN 1756-8919. E-ISSN 1756-8927
Institutional support: RVO:61388963
Keywords : computer-aided drug design * coronavirus * molecular docking * molecular dynamics simulations * Mpro * protease inhibitors * SARS-CoV-2 * virtual screening
OECD category: Biochemistry and molecular biology
Impact factor: 4.2, year: 2022
Method of publishing: Limited access
https://doi.org/10.4155/fmc-2023-0034
Permanent Link: https://hdl.handle.net/11104/0344832 - 9.0574520 - BFÚ 2024 RIV US eng J - Journal Article
Love, O. - Galindo-Murillo, R. - Zgarbová, M. - Šponer, Jiří - Jurečka, P. - Cheatham III, T. E.
Assessing the Current State of Amber Force Field Modifications for DNA ,2023 Edition.
Journal of Chemical Theory and Computation. Roč. 19, č. 13 (2023), s. 4299-4307. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * PARTICLE MESH EWALD * NUCLEIC-ACIDS
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 5.5, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jctc.3c00233
Permanent Link: https://hdl.handle.net/11104/0350087 - 10.0574386 - ÚT 2024 RIV NL eng J - Journal Article
Aminian, Ali - Vinš, Václav
Molecular simulations of transport properties of polar hydrofluoroethers: Force field development, fractional Stokes-Einstein and free volume relations.
Journal of Molecular Liquids. Roč. 389, November (2023), č. článku 122847. ISSN 0167-7322. E-ISSN 1873-3166
R&D Projects: GA ČR(CZ) GA22-03380S
Institutional support: RVO:61388998
Keywords : molecular dynamics simulations * transport properties * hydrofluoroether * free volume * stokes-einstein
OECD category: Thermodynamics
Impact factor: 6, year: 2022
Method of publishing: Limited access
https://www.sciencedirect.com/science/article/pii/S0167732223016525?via%3Dihub
Permanent Link: https://hdl.handle.net/11104/0349188