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dr inż. Rafał Madaj

Research Interests

  • Employing molecular docking techniques and molecular dynamics simulations in the analysis of conformational changes in proteins and protein-ligand complexes.
  • Mutations of Connexin 32 and their influence on gap junction conditioning the disease Charcot-Marie-Tooth type 1X.


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

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

Briefings in Bioinformatics, 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

Bioorganic Chemistry, 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

Processes, 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

Journal of Molecular Graphics and Modelling, 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

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

Biomolecules, 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

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

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

Abstract | Links | BibTeX