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dr inż. Rafał Madaj

Zainteresowania badawcze

  • Zastosowanie technik dokowania molekularnego oraz dynamiki molekularnej w analizie zmian konformacyjnych białek oraz kompleksów ligand-białko.
  • Mutacje Koneksyny 32 i ich wpływ na funkcjonalność kanału jonowego warunkującego chorobę Charcot-Marie-Tooth typu 1X.

Publikacje

Szustak, Marcin; Korkus, Eliza; Madaj, Rafal; Chworos, Arkadiusz; Dąbrowski, Grzegorz; Czaplicki, Sylwester; Tabandeh, Erfan; Maciejewska, Gabriela; Koziołkiewicz, Maria; Konopka, Iwona; Gliszczyńska, Anna; Gendaszewska-Darmach, Edyta

Lysophosphatidylcholines Enriched with cis and trans Palmitoleic Acid Regulate Insulin Secretion via GPR119 Receptor Journal Article

In: ACS Medicinal Chemistry Letters, vol. 15, no. 2, pp. 197-204, 2024.

Links | BibTeX

Madaj, Rafal; Gostyński, Bartłomiej; Chworos, Arkadiusz; Cypryk, Marek

Novichok Nerve Agents as Inhibitors of Acetylcholinesterase - In Silico Study of Their Non-Covalent Binding Affinity Journal Article

In: Molecules, vol. 29, no. 2, 2024, ISSN: 1420-3049.

Abstract | Links | BibTeX

Winski, Aleksander; Ludwiczak, Jan; Orlowska, Malgorzata; Madaj, Rafal; Kaminski, Kamil; Dunin-Horkawicz, Stanislaw

AlphaFold2 captures the conformational landscape of the HAMP signaling domain Journal Article

In: Protein Science, vol. 33, no. 1, pp. e4846, 2024.

Abstract | Links | BibTeX

Korkus, Eliza; Szustak, Marcin; Madaj, Rafal; Chworos, Arkadiusz; Drzazga, Anna; Koziołkiewicz, Maria; Dąbrowski, Grzegorz; Czaplicki, Sylwester; Konopka, Iwona; Gendaszewska-Darmach, Edyta

Trans-palmitoleic acid, a dairy fat biomarker, stimulates insulin secretion and activates G protein-coupled receptors with a different mechanism from the cis isomer Journal Article

In: Food Funct., vol. 14, no. 14, pp. 6496–6512, 2023, ISSN: 2042-650X.

Abstract | Links | BibTeX

Geoffrey, Ben AS.; Madaj, Rafał; Valluri, Pavan Preetham

QPoweredCompound2DeNovoDrugPropMax – a novel programmatic tool incorporating deep learning and in silico methods for automated in silico bio-activity discovery for any compound of interest Journal Article

In: Journal of Biomolecular Structure and Dynamics, pp. 1-8, 2022, ISSN: 0739-1102.

Abstract | Links | BibTeX

Kamiński, Kamil; Ludwiczak, Jan; Jasiński, Maciej; Bukala, Adriana; Madaj, Rafal; Szczepaniak, Krzysztof; Dunin-Horkawicz, Stanisław

Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins Journal Article

In: Briefings in Bioinformatics, vol. 23, 2022, ISSN: 1467-5463.

Abstract | Links | BibTeX

Szczupak, Patrycja; Radzikowska-Cieciura, Ewa; Kulik, Katarzyna; Madaj, Rafał; Sierant, Małgorzata; Krakowiak, Agnieszka; Nawrot, Barbara

Escherichia coli tRNA 2-selenouridine synthase SelU selects its prenyl substrate to accomplish its enzymatic function Journal Article

In: Bioorganic Chemistry, vol. 122, pp. 105739, 2022, ISSN: 00452068.

Abstract | Links | BibTeX

Madaj, Rafał; Sroczyński, Witold; Sójka, Michał; Olejnik, Tomasz P; Sobiecka, Elżbieta

Batch Mode Reactor for 3,5-Dinitrosalicylic Acid Degradation by Phanerochaete chrysosporium Journal Article

In: Processes, vol. 9, pp. 105, 2021, ISSN: 2227-9717.

Abstract | Links | BibTeX

Madaj, Rafal; Pawlowska, Roza; Chworos, Arkadiusz

In silico exploration of binding of selected bisphosphonate derivatives to placental alkaline phosphatase via docking and molecular dynamics Journal Article

In: Journal of Molecular Graphics and Modelling, vol. 103, pp. 107801, 2021, ISSN: 10933263.

Abstract | Links | BibTeX

Madaj, Rafal; Geoffrey, Ben; Sanker, Akhil; Valluri, Pavan Preetham

Target2DeNovoDrug: a novel programmatic tool for in silico -deep learning based de novo drug design for any target of interest Journal Article

In: Journal of Biomolecular Structure and Dynamics, pp. 1-6, 2021, ISSN: 0739-1102.

Abstract | Links | BibTeX

Madaj, Rafal; Gostynski, Bartlomiej; Pawlowska, Roza; Chworos, Arkadiusz

Tissue-Nonspecific Alkaline Phosphatase (TNAP) as the Enzyme Involved in the Degradation of Nucleotide Analogues in the Ligand Docking and Molecular Dynamics Approaches Journal Article

In: Biomolecules, vol. 11, pp. 1104, 2021, ISSN: 2218-273X.

Abstract | Links | BibTeX

Geoffrey, Ben; Sanker, Akhil; Madaj, Rafal; Tresanco, Mario Sergio Valdés; Upadhyay, Manish; Gracia, Judith

A program to automate the discovery of drugs for West Nile and Dengue virus—programmatic screening of over a billion compounds on PubChem, generation of drug leads and automated in silico modelling Journal Article

In: Journal of Biomolecular Structure and Dynamics, pp. 1-9, 2020, ISSN: 0739-1102.

Abstract | Links | BibTeX

Madaj, R; Sobiecka, E; Kalinowska, H

Lindane, kepone and pentachlorobenzene: chloropesticides banned by Stockholm convention Journal Article

In: International Journal of Environmental Science and Technology, vol. 15, pp. 471-480, 2018, ISSN: 1735-1472.

Abstract | Links | BibTeX