Search results
- 1.0584553 - ÚOCHB 2024 RIV US eng J - Journal Article
Vazdar, K. - Tempra, Carmelo - Olžyńska, A. - Biriukov, Denys - Cwiklik, Lukasz - Vazdar, M.
Stealthy Player in Lipid Experiments? EDTA Binding to Phosphatidylcholine Membranes Probed by Simulations and Monolayer Experiments.
Journal of Physical Chemistry B. Roč. 127, č. 24 (2023), s. 5462-5469. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT(CZ) LX22NPO5103
Institutional support: RVO:61388963
Keywords : chelating agents * force field * calcium
OECD category: Physical chemistry
Impact factor: 3.3, year: 2022
Method of publishing: Open access
https://doi.org/10.1021/acs.jpcb.3c03207
Permanent Link: https://hdl.handle.net/11104/0352462File Download Size Commentary Version Access 10.1021acs.jpcb.3c03207.pdf 1 2.9 MB Publisher’s postprint open-access - 2.0579727 - BC 2024 RIV CH eng J - Journal Article
Mikhnovets, I.E. - Holoubek, Jiří - Panina, I.S. - Kotouček, J. - Gvozdev, D.A. - Chumakov, S.P. - Krasilnikov, M.S. - Zhitlov, M.Y. - Gulyak, E.L. - Chistov, A.A. - Nikitin, T.D. - Korshun, V.A. - Efremov, R. G. - Alferova, V.A. - Růžek, Daniel - Eyer, Luděk - Ustinov, A.V.
Alkyl Derivatives of Perylene Photosensitizing Antivirals: Towards Understanding the Influence of Lipophilicity.
International Journal of Molecular Sciences. Roč. 24, č. 22 (2023), č. článku 16483. ISSN 1661-6596
R&D Projects: GA MŠMT(CZ) LX22NPO5103
Institutional support: RVO:60077344
Keywords : amphipathic fusion inhibitors * singlet oxygen generation * charmm force-field * photodynamic therapy * virus * gui * reproduction * dyes * antivirals * perylene * photosensitizers * singlet oxygen * lipophilicity
OECD category: Virology
Impact factor: 5.6, year: 2022
Method of publishing: Open access
https://www.mdpi.com/1422-0067/24/22/16483
Permanent Link: https://hdl.handle.net/11104/0348530File Download Size Commentary Version Access Mikhnovets_2023_IntJMolSci.pdf 1 5.8 MB Publisher’s postprint open-access - 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 - 4.0578099 - MBÚ 2024 RIV US eng J - Journal Article
Kulik, Natalia - Minofar, B. - Jugl, A. - Pekař, M.
Computational Study of Complex Formation between Hyaluronan Polymers and Polyarginine Peptides at Various Ratios.
Langmuir. Roč. 39, č. 40 (2023), s. 14212-14222. ISSN 0743-7463
Research Infrastructure: e-INFRA CZ II - 90254
Keywords : molecular-dynamics * force-field * acid * yasara * tool
OECD category: Physical chemistry
Impact factor: 3.9, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.langmuir.3c01318
Permanent Link: https://hdl.handle.net/11104/0347140 - 5.0572134 - BFÚ 2024 RIV US eng J - Journal Article
Zhang, Zhengyue - Šponer, Jiří - Bussi, G. - Mlýnský, Vojtech - Sulc, P. - Simmons, Ch. R. - Stephanopoulos, N. - Krepl, Miroslav
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.
Journal of Chemical Information and Modeling. Roč. 63, č. 9 (2023), s. 2794-2809. ISSN 1549-9596. E-ISSN 1549-960X
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : FORCE-FIELD * BRANCH MIGRATION * NUCLEIC-ACIDS
OECD category: Inorganic and nuclear chemistry
Impact factor: 5.6, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jcim.3c00358
Permanent Link: https://hdl.handle.net/11104/0349995 - 6.0571957 - ÚOCHB 2024 RIV US eng J - Journal Article
Fábián, Balázs - Vattulainen, I. - Javanainen, Matti
Protein Crowding and Cholesterol Increase Cell Membrane Viscosity in a Temperature Dependent Manner.
Journal of Chemical Theory and Computation. Roč. 19, č. 9 (2023), s. 2630-2643. ISSN 1549-9618. E-ISSN 1549-9626
Institutional support: RVO:61388963
Keywords : molecular dynamics simulations * lateral diffusion * force field
OECD category: Physical chemistry
Impact factor: 5.5, year: 2022
Method of publishing: Open access
https://doi.org/10.1021/acs.jctc.3c00060
Permanent Link: https://hdl.handle.net/11104/0342809 - 7.0571531 - BFÚ 2024 RIV US eng J - Journal Article
Kührová, P. - Mlýnský, Vojtech - Otyepka, M. - Šponer, Jiří - Banáš, P.
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. Roč. 63, č. 7 (2023), s. 2133-2146. ISSN 1549-9596. E-ISSN 1549-960X
R&D Projects: GA ČR(CZ) GA23-05639S
Institutional support: RVO:68081707
Keywords : AMBER FORCE-FIELD * NUCLEIC-ACIDS * CATION-BINDING
OECD category: Analytical chemistry
Impact factor: 5.6, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jcim.2c01438
Permanent Link: https://hdl.handle.net/11104/0346082 - 8.0571004 - ÚOCHB 2024 RIV US eng J - Journal Article
Phan, L. X. - Cruces Chamorro, Victor - Martinez-Seara, Hector - Crain, J. - Sansom, M. S. P. - Tucker, S. J.
Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin.
Biophysical Journal. Roč. 122, č. 8 (2023), s. 1548-1556. ISSN 0006-3495. E-ISSN 1542-0086
Institutional support: RVO:61388963
Keywords : molecular dynamics * software news * force field
OECD category: Physical chemistry
Impact factor: 3.4, year: 2022
Method of publishing: Open access
https://doi.org/10.1016/j.bpj.2023.03.026
Permanent Link: https://hdl.handle.net/11104/0342326 - 9.0569227 - BFÚ 2023 RIV US eng J - Journal Article
Pokorná, Pavlína - Krepl, Miroslav - Campagne, S. - Šponer, Jiří
Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations.
Journal of Physical Chemistry B. Roč. 126, č. 45 (2022), s. 9207-9221. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GA20-16554S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : FORCE-FIELD * NUCLEIC-ACIDS * AMBER * BACKBONE * BINDING
OECD category: Clinical neurology
Impact factor: 3.3, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jpcb.2c06168
Permanent Link: https://hdl.handle.net/11104/0340609 - 10.0561273 - ÚOCHB 2023 RIV US eng J - Journal Article
Ganguly, P. - Bubák, D. - Polák, J. - Fagan, P. - Dračínský, Martin - Van Der Vegt, N. F. A. - Heyda, J. - Shea, J. E.
Cosolvent Exclusion Drives Protein Stability in Trimethylamine N-Oxide and Betaine Solutions.
Journal of Physical Chemistry Letters. Roč. 13, č. 34 (2022), s. 7980-7986. ISSN 1948-7185
R&D Projects: GA ČR(CZ) GA22-15374S
Institutional support: RVO:61388963
Keywords : force-field * preferential interactions * glycine betaine
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 5.7, year: 2022
Method of publishing: Limited access
https://doi.org/10.1021/acs.jpclett.2c01692
Permanent Link: https://hdl.handle.net/11104/0333964