Výpis publikací

PLANAS IGLESIAS, Joan; Marika MAJEROVÁ; Daniel PLUSKAL; Michal VAŠINA; Jiří DAMBORSKÝ; Zbyněk PROKOP; Martin MAREK a David BEDNÁŘ. Automated Engineering Protein Dynamics via Loop Grafting: Improving Renilla Luciferase Catalysis. ACS Catalysis. WASHINGTON: American Chemical Society, 2025, roč. 15, č. 4, s. 3391-3404. ISSN 2155-5435. Dostupné z: https://dx.doi.org/10.1021/acscatal.4c06207.

OPÁLENÝ, Filip; Pavol ULBRICH; Joan PLANAS IGLESIAS; Jan BYŠKA; Jan ŠTOURAČ; David BEDNÁŘ; Katarína FURMANOVÁ a Barbora KOZLÍKOVÁ. Visual Support for the Loop Grafting Workflow on Proteins. IEEE Transactions on Visualization and Computer Graphics. United States: IEEE Computer Society, 2025, roč. 31, č. 1, s. 580-590. ISSN 1077-2626. Dostupné z: https://dx.doi.org/10.1109/TVCG.2024.3456401.

KHAN, Rayyan Tariq; Petra POKORNÁ; Jan DVORSKÝ; Simeon BORKO; Ihor AREFIEV; Joan PLANAS IGLESIAS; Adam DOBIÁŠ; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Veronika SZOTKOWSKÁ; Jaroslav ŠTĚRBA; Ondřej SLABÝ; Jiří DAMBORSKÝ; Stanislav MAZURENKO a David BEDNÁŘ. A computational workflow for analysis of missense mutations in precision oncology. JOURNAL OF CHEMINFORMATICS. ENGLAND: BMC, 2024, roč. 16, č. 1, s. 1-10. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-024-00876-3.

PLANAS IGLESIAS, Joan; Simeon BORKO; Jan SWIATKOWSKI; Matej ELIAS; Martin HAVLÁSEK; Ondrej SALAMON; Ekaterina GRAKOVA; Antonín KUNKA; Tomas MARTINOVIC; Jiří DAMBORSKÝ; Jan MARTINOVIC a David BEDNÁŘ. AggreProt: a web server for predicting and engineering aggregation prone regions in proteins. Nucleic Acids Research. Oxford: Oxford University Press, 2024, roč. 52, W1, s. "W159"-"W169", 11 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkae420.

KHAN, Rayyan Tariq; Petra POKORNÁ; Jan DVORSKÝ; Simeon BORKO; Adam DOBIÁŠ; Joan PLANAS IGLESIAS; Stanislav MAZURENKO; Ihor AREFIEV; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Veronika SZOTKOWSKÁ; Jaroslav ŠTĚRBA; Jiří DAMBORSKÝ; Ondřej SLABÝ a David BEDNÁŘ. Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO. Computational and Structural Biotechnology Journal. AMSTERDAM: Elsevier, 2024, roč. 24, December 2024, s. 734-738. ISSN 2001-0370. Dostupné z: https://dx.doi.org/10.1016/j.csbj.2024.11.026.

MARQUES, Sérgio Manuel; Petr KOUBA; Anthony Thomas P LEGRAND; Jiri SEDLAR; Lucas DISSON; Joan PLANAS IGLESIAS; Zainab Kemi SANUSI; Antonín KUNKA; Jiří DAMBORSKÝ; Tomas PAJDLA; Zbyněk PROKOP; Stanislav MAZURENKO; Josef SIVIC a David BEDNÁŘ. CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS AU. WASHINGTON: AMER CHEMICAL SOC, 2024, roč. 4, č. 6, s. 2228-2245. ISSN 2691-3704. Dostupné z: https://dx.doi.org/10.1021/jacsau.4c00182.

ŠTOURAČ, Jan; Simeon BORKO; Rayyan Tariq KHAN; Petra POKORNÁ; Adam DOBIÁŠ; Joan PLANAS IGLESIAS; Stanislav MAZURENKO; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Veronika SZOTKOWSKÁ; Jaroslav ŠTĚRBA; Ondřej SLABÝ; Jiří DAMBORSKÝ a David BEDNÁŘ. PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. Briefings in Bioinformatics. Oxford University Press, 2024, roč. 25, č. 1, s. 1-10. ISSN 1467-5463. Dostupné z: https://dx.doi.org/10.1093/bib/bbad441.

NEMERGUT, Michal; Sérgio Manuel MARQUES; Lukáš UHRÍK; Tereza VÁŇOVÁ; Markéta NEZVEDOVÁ; Darshak Chandulal GADARA; Durga JHA; Jan TULIS; Veronika NOVÁKOVÁ; Joan PLANAS IGLESIAS; Antonín KUNKA; Anthony Thomas P LEGRAND; Hana HŘÍBKOVÁ; Veronika POSPÍŠILOVÁ; Jiří SEDMÍK; Jan RAŠKA; Zbyněk PROKOP; Jiří DAMBORSKÝ; Dáša BOHAČIAKOVÁ; Zdeněk SPÁČIL; Lenka HERNYCHOVÁ; David BEDNÁŘ a Martin MAREK. Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s Disease drug candidate. Molecular Neurodegeneration. England: BMC, 2023, roč. 18, č. 1, s. 1-25. ISSN 1750-1326. Dostupné z: https://dx.doi.org/10.1186/s13024-023-00620-9.

GOHL, Patrick; Jaume BONET; Oriol FORNES; Joan PLANAS IGLESIAS; Narcıs FERNANDEZ-FUENTES a Baldo OLIVA. SBILib: a handle for protein modeling and engineering. Bioinformatics. Oxford University Press, 2023, roč. 39, č. 10, s. 1-3. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btad613.

UHRIK, Lukas; Tomas HENEK; Joan PLANAS IGLESIAS; Josef KUCERA; Jiří DAMBORSKÝ; Martin MAREK a Lenka HERNYCHOVA. Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry. In Ângela Sousa, Luis Passarinha. Advanced Methods in Structural Biology. New York: Springer Nature, 2023, s. 293-318. 1. ISBN 978-1-0716-3146-1. Dostupné z: https://dx.doi.org/10.1007/978-1-0716-3147-8_18.

BOUCHALOVÁ, Pavla; Lucia SOMMEROVÁ; David POTĚŠIL; Andrea MARTIŠOVÁ; Petr LAPČÍK; Veronika BRYCHTOVÁ; Alexander SCHERL; Petr VOŇKA; Joan PLANAS IGLESIAS; Eric CHEVET; Pavel BOUCHAL a Roman HRSTKA. Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells. Molecular & Cellular Proteomics. American Society for Biochemistry and Molecular Biology, 2022, roč. 21, č. 2, s. 1-19. ISSN 1535-9484. Dostupné z: https://dx.doi.org/10.1016/j.mcpro.2021.100188.

PLANAS IGLESIAS, Joan; Filip OPÁLENÝ; Pavol ULBRICH; Jan ŠTOURAČ; Zainab Kemi SANUSI; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Andrea SMITH; Jan BYŠKA; Jiří DAMBORSKÝ; Barbora KOZLÍKOVÁ a David BEDNÁŘ. LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic acids research. Oxford: Oxford University Press, 2022, roč. 50, W1, s. "W465"-"W473", 9 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkac249.

PLANAS IGLESIAS, Joan; Filip OPÁLENÝ; Pavol ULBRICH; Jan ŠTOURAČ; Zainab Kemi SANUSI; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; A. SCHENKMAYEROVÁ; Jan BYŠKA; Jiří DAMBORSKÝ; Barbora KOZLÍKOVÁ a David BEDNÁŘ. Nástroj LoopGrafter. 2022.

VAŠINA, Michal; Jan VELECKÝ; Joan PLANAS IGLESIAS; Sérgio Manuel MARQUES; Jana ŠKAŘUPOVÁ; Jiří DAMBORSKÝ; David BEDNÁŘ; Stanislav MAZURENKO a Zbyněk PROKOP. Tools for computational design and high-throughput screening of therapeutic enzymes. ADVANCED DRUG DELIVERY REVIEWS. NETHERLANDS: ELSEVIER, 2022, roč. 183, April 2022, s. 1-16. ISSN 0169-409X. Dostupné z: https://dx.doi.org/10.1016/j.addr.2022.114143.

PLANAS IGLESIAS, Joan; Sérgio Manuel MARQUES; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Miloš MUSIL; Jan ŠTOURAČ; Jiří DAMBORSKÝ a David BEDNÁŘ. Computational design of enzymes for biotechnological applications. Biotechnology Advances. OXFORD: Elsevier, 2021, roč. 47, March–April, s. 1-22. ISSN 0734-9750. Dostupné z: https://dx.doi.org/10.1016/j.biotechadv.2021.107696.

DAMBORSKÝ, Jiří; David BEDNÁŘ; Zbyněk PROKOP; Martin MAREK; Stanislav MAZURENKO; Jan ŠTOURAČ; Sérgio Manuel MARQUES; Gabriela Filipa FONSECA PINTO; Joan PLANAS IGLESIAS; Miloš MUSIL; Jiří HON; Ondřej VÁVRA; Rayyan Tariq KHAN; Jiří FILIPOVIČ a Barbora KOZLÍKOVÁ. Computational enzyme design for metabolic engineering. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

MARKOVÁ, Klára; Antonín KUNKA; Klaudia CHMELOVÁ; Martin HAVLÁSEK; Petra BABKOVÁ; Sérgio Manuel MARQUES; Michal VAŠINA; Joan PLANAS IGLESIAS; Radka CHALOUPKOVÁ; David BEDNÁŘ; Zbyněk PROKOP; Jiří DAMBORSKÝ a Martin MAREK. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2021, roč. 11, č. 21, s. 12864-12885. ISSN 2155-5435. Dostupné z: https://dx.doi.org/10.1021/acscatal.1c03343.

MAREK, Martin; Jiří DAMBORSKÝ; David BEDNÁŘ; Daniel PLUSKAL; Marika MAJEROVÁ a Joan PLANAS IGLESIAS. Designované a syntetizované geny kódující nově zkonstruované proteinové katalyzátory (luciferázy) s ověřenými vlastnostmi. 2021.

TOUL, Martin; Andrea SMITH; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Martin MAREK; Lenka HERNYCHOVÁ; Veronika LIŠKOVÁ; Daniel PLUSKAL; Stephane EMOND; Mark DÖRR; Joan PLANAS IGLESIAS; Radka CHALOUPKOVÁ; David BEDNÁŘ; Zbyněk PROKOP; Uwe T. BORNSCHEUER; Florian HOLLFELDER a Jiří DAMBORSKÝ. Engineering protein dynamics for the understanding of divergent evolution of the Renilla luciferase. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

SCHENKMAYEROVÁ, Andrea; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Martin TOUL; Martin MAREK; Lenka HERNYCHOVÁ; Joan PLANAS IGLESIAS; Veronika LIŠKOVÁ; Daniel PLUSKAL; Michal VAŠINA; Stephane EMOND; Mark DÖRR; Radka CHALOUPKOVÁ; David BEDNÁŘ; Zbyněk PROKOP; Florian HOLLFELDER; Uwe T. BORNSCHEUER a Jiří DAMBORSKÝ. Engineering the protein dynamics of an ancestral luciferase. Nature Communications. London: Nature Publishing Group, 2021, roč. 12, č. 1, s. 3616-3631. ISSN 2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-021-23450-z.

MIRELA-BOTA, Patricia; Joaquim AGUIRRE-PLANS; Alberto MESEGUER; Cristiano GALLETTI; Joan SEGURA; Joan PLANAS IGLESIAS; Javi GARCIA-GARCIA; Emre GUNEY; Baldo OLIVA a Narcis FERNANDEZ-FUENTES. Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data. Journal of Molecular Biology. London: Elsevier Science Ltd, 2021, roč. 433, č. 11, s. 166656-166666. ISSN 0022-2836. Dostupné z: https://dx.doi.org/10.1016/j.jmb.2020.09.015.

MARQUES, Sérgio Manuel; Joan PLANAS IGLESIAS a Jiří DAMBORSKÝ. Web-based tools for computational enzyme design. Current Opinion in Structural Biology. London: Elsevier Science Ltd., 2021, roč. 69, August 2021, s. 19-34. ISSN 0959-440X. Dostupné z: https://dx.doi.org/10.1016/j.sbi.2021.01.010.

KUMAR, Lokender; Joan PLANAS IGLESIAS; Chase HARMS; Sumaer KAMBOJ; Derek WRIGHT; Judith KLEIN-SEETHARAMAN a K.Susanta SARKAR. Activity-dependent interdomain dynamics of matrix metalloprotease-1 on fibrin. Scientific Reports. Berlin: Nature Research, 2020, roč. 10, č. 1, s. 1-14. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-020-77699-3.

KUMAR, Lokender; Anthony NASH; Chase HARMS; Joan PLANAS IGLESIAS; Derek WRIGHT; Judith KLEIN-SEETHARAMAN a Susanta K SARKAR. Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1. Biophysical Journal. Bethesda, USA: Biophysical Society, 2020, roč. 119, č. 2, s. 360-374. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2020.06.010.

MITCHELL, James; Fernanda BALEM; Kalyan TIRUPULA; David MAN; Harpreet Kaur DHIMAN; Naveena YANAMALA; Julian OLLESCH; Joan PLANAS IGLESIAS; Barbara J. JENNINGS; Klaus GERWERT; Alessandro IANNACCONE a Judith KLEIN-SEETHARAMAN. Comparison of the molecular properties of retinitis pigmentosa P23H and N15S amino acid replacements in rhodopsin. Plos one. San Francisco: Public Library of Science, 2019, roč. 14, č. 5, s. 1-14. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0214639.

CHRÁST, Lukáš; K. TRATSIAK; Joan PLANAS IGLESIAS; Lukáš DANIEL; T. PRUDNIKOVA; Jan BREZOVSKÝ; David BEDNÁŘ; I.K. SMATANOVA; Radka CHALOUPKOVÁ a Jiří DAMBORSKÝ. Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. Microorganisms. Basel: MDPI, 2019, roč. 7, č. 11, s. 1-20. ISSN 2076-2607. Dostupné z: https://dx.doi.org/10.3390/microorganisms7110498.