Search results
- 1.0585960 - ÚOCHB 2025 RIV AT eng C - Conference Paper (international conference)
Bushuiev, A. - Bushuiev, Roman - Sedlář, J. - Pluskal, Tomáš - Damborský, J. - Mazurenko, S. - Šivic, J.
Revealing data leakage in protein interaction benchmarks.
GEM-2024. ICLR 2024 Workshop on Generative and Experimental Perspectives for Biomolecular Design. Vienna: ICLR, 2024.
[ICLR 2024. International Conference on Learning Representations /12./. Vienna (AT), 07.05.2024-11.05.2024]
R&D Projects: GA MŠMT(CZ) LM2023055; GA ČR(CZ) GM21-11563M
EU Projects: European Commission(XE) 891397 - KavaTarget
Research Infrastructure: e-INFRA CZ II - 90254; RECETOX RI II - 90269
Institutional support: RVO:61388963
Keywords : protein-protein interactions * data leakage * benchmarks * data splits
OECD category: Other biological topics
https://openreview.net/forum?id=ORMXYUK5IY
Permanent Link: https://hdl.handle.net/11104/0353594File Download Size Commentary Version Access 0585960.pdf 0 1.7 MB Publisher’s postprint open-access - 2.0585897 - ÚOCHB 2025 RIV AT eng C - Conference Paper (international conference)
Bushuiev, A. - Bushuiev, Roman - Kouba, P. - Filkin, A. - Gabrielová, M. - Gabriel, M. - Sedlář, J. - Pluskal, Tomáš - Damborský, J. - Mazurenko, S. - Šivic, J.
Learning to design protein-protein interactions with enhanced generalization.
ICLR 2024. The Twelfth International Conference on Learning Representations. Vienna: ICLR, 2024.
[ICLR 2024. International Conference on Learning Representations /12./. Vienna (AT), 07.05.2024-11.05.2024]
R&D Projects: GA MŠMT(CZ) LM2023055; GA ČR(CZ) GM21-11563M
EU Projects: European Commission(XE) 891397 - KavaTarget
Research Infrastructure: e-INFRA CZ II - 90254; RECETOX RI II - 90269
Institutional support: RVO:61388963
Keywords : protein-protein interactions * protein design * generalization * self-supervised learning * equivariant 3D representations
OECD category: Other biological topics
https://openreview.net/forum?id=xcMmebCT7s
Permanent Link: https://hdl.handle.net/11104/0353542File Download Size Commentary Version Access 0585897.pdf 0 9.5 MB Publisher’s postprint open-access - 3.0574534 - BTÚ 2024 RIV CH eng J - Journal Article
Pham, Phuong Ngoc - Zahradník, J. - Kolářová, Lucie - Schneider, Bohdan - Fuertes, Gustavo
Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light.
Frontiers in molecular biosciences. Roč. 10, JUL 7 2023 (2023), č. článku 1214235. E-ISSN 2296-889X
R&D Projects: GA MŠMT LM2023042; GA MŠMT EF15_003/0000447; GA MŠMT(CZ) EF18_046/0015974; GA MŠMT LX22NPO5102
Institutional support: RVO:86652036
Keywords : protein-protein interactions (PPI) * interleukin-24 * cytokines * optobinders * genetically encoded non-canonical amino acids (ncAA) * photocaged proteins
OECD category: Biochemistry and molecular biology
Impact factor: 5, year: 2022
Method of publishing: Open access
https://www.frontiersin.org/articles/10.3389/fmolb.2023.1214235/full
Permanent Link: https://hdl.handle.net/11104/0345655 - 4.0570494 - ÚOCHB 2024 RIV GB eng J - Journal Article
Selvaraj, C. - Dinesh, Dhurvas Chandrasekaran - Pedone, E. M. - Alothaim, A. S. - Vijayakumar, R. - Rudhra, O. - Singh, S. K.
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors.
Briefings in Functional Genomics. Roč. 22, č. 2 (2023), s. 227-240. ISSN 2041-2649. E-ISSN 2041-2657
Institutional support: RVO:61388963
Keywords : SARS-CoV-2 * ORF8 * SARS-CoV * dimer * disulfide bond * covid-19 * protein-protein interactions * molecular dynamics * MHC-1 * immune evasion * viral peptides
OECD category: Biochemistry and molecular biology
Impact factor: 4, year: 2022
Method of publishing: Limited access
https://doi.org/10.1093/bfgp/elac046
Permanent Link: https://hdl.handle.net/11104/0341789 - 5.0562211 - FGÚ 2023 RIV CH eng J - Journal Article
Obšilová, Veronika - Obšil, T.
Structural insights into the functional roles of 14-3-3 proteins.
Frontiers in molecular biosciences. Roč. 9, Sep 16 (2022), č. článku 1016071. E-ISSN 2296-889X
R&D Projects: GA ČR(CZ) GA21-02080S; GA ČR(CZ) GA19-00121S
Institutional support: RVO:67985823
Keywords : 14-3-3 proteins * protein-protein interactions * phosphorylation * molecular mechanism * scaffolding * adaptor protein
OECD category: Biochemistry and molecular biology
Impact factor: 5, year: 2022
Method of publishing: Open access
https://doi.org/10.3389/fmolb.2022.1016071
Permanent Link: https://hdl.handle.net/11104/0334618 - 6.0551156 - ÚOCHB 2022 CZ eng A - Abstract
Sýs, Jakub - Hubálek, Martin - Cvačka, Josef
Proteins Structure and Interactions Studied by Hydrogen Deuterium Exchange Mass Spectrometry.
Prague Meeting on Historical Perspectives of Mass Spectrometry, Book of Abstracts. Praha: Ústav organické chemie a biochemie AV ČR, v. v. i., 2021 - (Hoskovec, M.; Cvačka, J.). s. 28. ISBN 978-80-86241-66-1.
[Prague Meeting on Historical Perspectives of Mass Spectrometry. 13.10.2021-14.10.2021, Praha]
R&D Projects: GA MŠMT(CZ) EF16_019/0000729
Institutional support: RVO:61388963
Keywords : proteins * hydrogen-deuterium exchange * protein-protein interactions
OECD category: Biochemistry and molecular biology
http://ms-prague2021.uochb.cas.cz/assets/pdf/BoA_final.pdf
Permanent Link: http://hdl.handle.net/11104/0326603 - 7.0550981 - ÚOCHB 2022 CZ eng A - Abstract
Sýs, Jakub - Hubálek, Martin - Boušová, Kristýna - Vondrášek, Jiří
First Year of Hydrogen-Deuterium Exchange at IOCB: The effect of domain order on fusion two-domain proteins structure.
7. Neformální proteomické setkání. Hradec Králové: Proteomická sekce České společnosti pro biochemii a molekulární biologii, 2021. s. 25.
[Neformální proteomické setkání /7./. 25.11.2021-26.11.2021, Hradec Králové]
R&D Projects: GA MŠMT(CZ) EF16_019/0000729
Institutional support: RVO:61388963
Keywords : hydrogen-deuterium exchange * proteins * protein-protein interactions
OECD category: Biochemistry and molecular biology
https://drive.google.com/file/d/13VvDDFQMpDf0B2WoucYAMtDB5UCidlHk/view
Permanent Link: http://hdl.handle.net/11104/0326258 - 8.0544813 - ÚOCHB 2022 RIV GB eng J - Journal Article
Li, M. - Srp, Jaroslav - Mareš, Michael - Wlodawer, A. - Gustchina, A.
Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI.
Acta Crystallographica Section D-Structural Biology. Roč. 77, č. 8 (2021), s. 1084-1098. ISSN 2059-7983. E-ISSN 2059-7983
R&D Projects: GA MŠMT(CZ) EF16_019/0000729
Institutional support: RVO:61388963
Keywords : proteases * kallikreins * trypsin * chymotrypsin * plant Kunitz inhibitors * protein–protein interactions * Bauhinia bauhinioides * BbKI * human kallikrein 4
OECD category: Biochemistry and molecular biology
Impact factor: 5.699, year: 2021
Method of publishing: Limited access
https://doi.org/10.1107/S2059798321006483
Permanent Link: http://hdl.handle.net/11104/0321620 - 9.0543494 - MBÚ 2022 RIV GB eng J - Journal Article
Del Amo-Maestro, L. - Sagar, A. - Pompach, Petr - Goulas, T. - Scavenius, C. - Ferrero, D. S. - Castrillo-Briceno, M. - Taules, M. - Enghild, J. J. - Bernado, P. - Gomis-Ruth, F.X.
An Integrative Structural Biology Analysis of Von Willebrand Factor Binding and Processing by ADAMTS-13 in Solution.
Journal of Molecular Biology. Roč. 433, č. 13 (2021), č. článku 166954. ISSN 0022-2836. E-ISSN 1089-8638
R&D Projects: GA MŠMT(CZ) ED1.1.00/02.0109
EU Projects: European Commission(XE) 823839 - EPIC-XS
Research Infrastructure: CIISB II - 90127
Institutional support: RVO:61388971
Keywords : protein-protein interactions * metallopeptidase * biophysical techniques * platelet aggregation * blood coagulation
OECD category: Biochemistry and molecular biology
Impact factor: 6.151, year: 2021
Method of publishing: Open access
https://www.sciencedirect.com/science/article/pii/S0022283621001558
Permanent Link: http://hdl.handle.net/11104/0320685 - 10.0541951 - BFÚ 2022 RIV GB eng J - Journal Article
Clery, A. - Krepl, Miroslav - Nguyen, C. K. X. - Moursy, A. - Jorjani, H. - Katsantoni, M. - Okoniewski, M. - Mittal, N. - Zavolan, M. - Šponer, Jiří - Allain, F.H.T.
Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing.
Nature Communications. Roč. 12, č. 1 (2021), č. článku 428. E-ISSN 2041-1723
R&D Projects: GA ČR(CZ) GA20-16554S
Institutional support: RVO:68081707
Keywords : pre-messenger-rna * spinal muscular-atrophy * protein-protein interactions * nmr structure determination * sr protein * recognition motifs
OECD category: Physical chemistry
Impact factor: 17.694, year: 2021
Method of publishing: Open access
https://www.nature.com/articles/s41467-020-20481-w
Permanent Link: http://hdl.handle.net/11104/0319465