Search results
- 1.0562066 - ÚOCHB 2023 RIV US eng J - Journal Article
Vymětal, Jiří - Vondrášek, Jiří
Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules.
Journal of Chemical Information and Modeling. Roč. 62, č. 19 (2022), s. 4783-4798. ISSN 1549-9596. E-ISSN 1549-960X
R&D Projects: GA ČR(CZ) GA19-03488S; GA MŠMT(CZ) EF16_019/0000729
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388963
Keywords : Monte-carlo simulation * molecular dynamics * alanine dipeptidea
OECD category: Biochemistry and molecular biology
Impact factor: 5.6, year: 2022
Method of publishing: Limited access
https://doi.org/10.1021/acs.jcim.2c00370
Permanent Link: https://hdl.handle.net/11104/0334483 - 2.0559713 - ÚOCHB 2023 RIV US eng J - Journal Article
Vymětal, Jiří - Mertová, Kateřina - Boušová, Kristýna - Šulc, Josef - Tripsianes, K. - Vondrášek, Jiří
Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x-ray reference structures as a prediction benchmark.
Proteins-Structure, Function and Bioinformatics. Roč. 90, č. 12 (2022), s. 2067-2079. ISSN 0887-3585. E-ISSN 1097-0134
R&D Projects: GA MŠMT(CZ) LM2018131; GA MŠMT(CZ) EF16_019/0000729; GA ČR(CZ) GA19-03488S
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388963
Keywords : 3D structure prediction * fusion proteins * molecular simulations * X-ray crystallography
OECD category: Biochemistry and molecular biology
Impact factor: 2.9, year: 2022
Method of publishing: Open access
https://doi.org/10.1002/prot.26398
Permanent Link: https://hdl.handle.net/11104/0332921 - 3.0559020 - ÚOCHB 2023 RIV GB eng J - Journal Article
Tretyachenko, V. - Vymětal, Jiří - Neuwirthova, T. - Vondrášek, Jiří - Fujishima, K. - Hlouchová, Klára
Modern and prebiotic amino acids support distinct structural profiles in proteins.
Open Biology. Roč. 12, č. 6 (2022), č. článku 220040. E-ISSN 2046-2441
Institutional support: RVO:61388963
Keywords : protein sequence space * protein structure * amino acid alphabet * genetic code evolution * random proteins
OECD category: Biochemistry and molecular biology
Impact factor: 5.8, year: 2022
Method of publishing: Open access
https://doi.org/10.1098/rsob.220040
Permanent Link: https://hdl.handle.net/11104/0332442 - 4.0556398 - ÚOCHB 2023 RIV US eng J - Journal Article
Boušová, Kristýna - Zouharová, Monika - Heřman, P. - Vymětal, Jiří - Vetýšková, Veronika - Jirásková, Kateřina - Vondrášek, Jiří
TRPM5 Channel Binds Calcium-Binding Proteins Calmodulin and S100A1.
Biochemistry. Roč. 61, č. 6 (2022), s. 413-423. ISSN 0006-2960
Institutional support: RVO:61388963
Keywords : ion channel * ryanodine receptor * N-terminus
OECD category: Biochemistry and molecular biology
Impact factor: 2.9, year: 2022
Method of publishing: Limited access
https://doi.org/10.1021/acs.biochem.1c00647
Permanent Link: http://hdl.handle.net/11104/0331043 - 5.0544133 - ÚOCHB 2022 RIV GB eng J - Journal Article
Vymětal, Jiří - Jakubec, Dávid - Galgonek, Jakub - Vondrášek, Jiří
Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures.
Nucleic Acids Research. Roč. 49, W1 (2021), W15-W20. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA MŠMT(CZ) LM2018131; GA MŠMT(CZ) EF16_019/0000729; GA ČR(CZ) GA19-03488S; GA MŠMT(CZ) LM2018131
Institutional support: RVO:61388963
Keywords : homeodomain * proteins * residues
OECD category: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Impact factor: 19.160, year: 2021
Method of publishing: Open access
https://doi.org/10.1093/nar/gkab377
Permanent Link: http://hdl.handle.net/11104/0321176
Research data: GitHub - 6.0538306 - ÚOCHB 2022 RIV GB eng J - Journal Article
Zouharová, Monika - Vymětal, Jiří - Bednárová, Lucie - Vaněk, O. - Herman, P. - Vetýšková, Veronika - Poštulková, Klára - Lingstaadas, P. S. - Vondrášek, Jiří - Boušová, Kristýna
Intrinsically disordered protein domain of human ameloblastin in synthetic fusion with calmodulin increases calmodulin stability and modulates its function.
International Journal of Biological Macromolecules. Roč. 168, Jan 31 (2021), s. 1-12. ISSN 0141-8130. E-ISSN 1879-0003
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388963
Keywords : calmodulin * fusion protein * intrinsically disordered protein (IDP) * ameloblastin
OECD category: Biochemistry and molecular biology
Impact factor: 8.025, year: 2021
Method of publishing: Limited access
https://doi.org/10.1016/j.ijbiomac.2020.11.216
Permanent Link: http://hdl.handle.net/11104/0316306 - 7.0536820 - ÚOCHB 2021 RIV CH eng J - Journal Article
Vetýšková, Veronika - Zouharová, Monika - Bednárová, Lucie - Vaněk, O. - Sázelová, Petra - Kašička, Václav - Vymětal, Jiří - Srp, Jaroslav - Rumlová, M. - Charnavets, Tatsiana - Poštulková, Klára - Reseland, J. E. - Boušová, Kristýna - Vondrášek, Jiří
Characterization of AMBN I and II Isoforms and Study of Their Ca2+-Binding Properties.
International Journal of Molecular Sciences. Roč. 21, č. 23 (2020), č. článku 9293. E-ISSN 1422-0067
R&D Projects: GA MŠMT(CZ) EF16_019/0000729; GA MŠMT(CZ) LM2018127
Institutional support: RVO:61388963 ; RVO:86652036
Keywords : ameloblastin * biomineralization * oligomerization * calcium binding * intrinsically disordered protein (IDPs)
OECD category: Biochemistry and molecular biology; Biochemistry and molecular biology (BTO-N)
Impact factor: 5.924, year: 2020
Method of publishing: Open access
https://doi.org/10.3390/ijms21239293
Permanent Link: http://hdl.handle.net/11104/0314572 - 8.0508837 - ÚOCHB 2020 RIV CH eng J - Journal Article
Vymětal, Jiří - Vondrášek, Jiří - Hlouchová, Klára
Sequence Versus Composition: What Prescribes IDP Biophysical Properties?
Entropy. Roč. 21, č. 7 (2019), č. článku 654. E-ISSN 1099-4300
R&D Projects: GA MŠMT(CZ) EF16_019/0000729; GA MŠMT(CZ) LM2015047
Institutional support: RVO:61388963
Keywords : IDP * IDR * sequence randomization * secondary structure prediction * aggregation propensity
OECD category: Biochemistry and molecular biology
Impact factor: 2.494, year: 2019
Method of publishing: Open access
https://www.mdpi.com/1099-4300/21/7/654
Permanent Link: http://hdl.handle.net/11104/0299640 - 9.0502462 - ÚOCHB 2020 RIV US eng J - Journal Article
Culka, Martin - Galgonek, Jakub - Vymětal, Jiří - Vondrášek, Jiří - Rulíšek, Lubomír
Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective.
Journal of Physical Chemistry B. Roč. 123, č. 6 (2019), s. 1215-1227. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GA17-24155S
Institutional support: RVO:61388963
Keywords : molecular dynamics * hydrogen exchange * basis sets
OECD category: Physical chemistry
Impact factor: 2.857, year: 2019
Method of publishing: Limited access
https://pubs.acs.org/doi/10.1021/acs.jpcb.8b09245
Permanent Link: http://hdl.handle.net/11104/0296497 - 10.0501431 - ÚOCHB 2020 RIV US eng J - Journal Article
Vymětal, Jiří - Jurásková, Veronika - Vondrášek, Jiří
AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation.
Journal of Chemical Theory and Computation. Roč. 15, č. 1 (2019), s. 665-679. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT(CZ) EF16_019/0000729; GA MŠMT(CZ) LM2015047
Institutional support: RVO:61388963
Keywords : intrinsically disordered proteins * molecular dynamics simulations * amino acids
OECD category: Physical chemistry
Impact factor: 5.011, year: 2019
Method of publishing: Limited access
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00715
Permanent Link: http://hdl.handle.net/11104/0296233