Bioinformatics Laboratory


Head
PhD Michał Koliński,  (+48) 22 849 93 58, This email address is being protected from spambots. You need JavaScript enabled to view it..

Research staff
PhD Beata Sokołowska, (+48) 22 849 93 58, This email address is being protected from spambots. You need JavaScript enabled to view it.
PhD Wojciech Puławski, (+48) 22 849 93 58, This email address is being protected from spambots. You need JavaScript enabled to view it.

Graduate students
MSc Urszula Orzeł This email address is being protected from spambots. You need JavaScript enabled to view it.

Technical staff
Grzegorz Firlik, (+48) 22 849 93 58, This email address is being protected from spambots. You need JavaScript enabled to view it.

Research profile
• application of multi-scale simulation methods for modeling of complex molecular systems,
• study of activation and signaling process of GPCRs,
• prediction of protein structure and study of protein-protein interactions,
• molecular modeling of biological membranes,
• application of molecular docking in drug design and discovery,
• analysis of spatial structure of biopolymers, applications of deep learning in structural biology,
• application of machine learning approach in the mathematical or statistical modelling and analysis of physiological systems in the clinic and other types of biomedical problems, including selected aspects based on VR solutions.

Grants
• "Analysis of similarity of biopolymer structures using descriptors of local structure", 2011/03/D/NZ2/02004, PhD Paweł Daniluk, 2012 – 2017,
• "Study of signaling of GPCRs using multi-scale molecular dynamics simulations", IP2012016372, PhD Michał Koliński, 2014-2016,
• „Development of a method for the structure prediction of GPCRs complexes with agonists and antagonists, including the ligand-induced alternations of the receptor structure", 2011/01/D/NZ2/05314, PhD Michał Koliński, 2012-2016.

Collaboration
domestic
• Faculty of Chemistry, University of Warsaw, Warsaw
• Faculty of Physics, University of Warsaw, Warsaw
• Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw
• Department of Biopharmacy, Medical University of Lublin, Lublin
• Biological and Chemical Research Centre, University of Warsaw, Warsaw
• Rheumatology Clinic and Outpatient Department, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw,
• Faculty of Physics and Applied Informatics, University of Łódź, Łódź.
foreign
• Department of Chemistry, Iowa State University, Ames, USA

Research equipment
• computer cluster comprising: 4 computing nodes (16-core processors), 16 computing nodes (12-core processors) equipped with GPUs.

Research methods
• Molecular modeling (multi-scale methods),
• Application of Molecular Dynamics simulations,
• Molecular docking,
• Predicting the structure of proteins and their complexes (comparative and ab initio methods).

Selected publications

  • Szulczyk D, Woziński M, Koliński M, Kmiecik S, Głogowska A, Augustynowicz-Kopeć E, A Dobrowolski M, Roszkowski P, Struga M and Ciura K: Menthol- and thymol-based ciprofloxacin derivatives against Mycobacterium tuberculosis: in vitro activity, lipophilicity, and computational studies. Scientific Reports, 2023, 16328(13).
  • Pulawski W, Kolinski A, Kolinski M: Integrative modeling of diverse protein-peptide systems using CABS-dock. PLOS Computational Biology, 2023, 19(7): e1011275.
  • Struga M, Roszkowski P, Bielenica A, Otto-Ślusarczyk D, Stępień K, Stefańska J, Zabost A, Augustynowicz-Kopeć E, Koliński M, Kmiecik S, Myslovska A, and Wrzosek M: N-Acylated Ciprofloxacin Derivatives: Synthesis and In Vitro Biological Evaluation as Antibacterial and Anticancer Agents. ACS Omega, 2023.
  • Maciag M, Plazinski W, Pulawski W, Kolinski M, Jozwiak K, Plazinska A: A comprehensive pharmacological analysis of fenoterol and its derivatives to unravel the role of β2-adrenergic receptor in zebrafish. Biomedicine & Pharmacotherapy. 2023, 60, 114355.
  • Sokołowska, B. Impact of Virtual Reality Cognitive and Motor Exercises on Brain Health.Int. J. Environ. Res. Public Health2023,20, 4150. DOI:10.3390/ijerph20054150.
  • Kurcinski M, Badaczewska‐Dawid A, Kolinski M, Kolinski A, Kmiecik S. Flexible docking of peptides to proteins using CABS‐dock. Protein Science. 2020,29:211-222. DOI:10.1002/pro.3771
  • Koliński M, Kmiecik S, Dec R, Piejko M, Mak P, Dzwolak W. Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulation. International Journal of Biological Macromolecules 2020,149:1151-1160. DOI:10.1016/j.ijbiomac.2020.01.253
  • Dec R, Kolinski M, Kouza M, Dzwolak W. Rapid self-association of highly amyloidogenic H-fragments of insulin: Experiment and molecular dynamics simulations. Int J Biol Macromol 2020,150:894-903. DOI:10.1016/j.ijbiomac.2020.02.153
  • Badaczewska-Dawid A, Kmiecik S, Kolinski M. Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement. Briefings in Bioinformatics, bbaa109, 2020. DOI:10.1093/bib/bbaa109
  • Dec R, Kolinski M, Dzwolak W. Beyond amino acid sequence: disulfide bonds and the origins of the extreme amyloidogenic properties of insulin's H-fragment. FEBS J 2019,286:3194-3205. DOI:10.1111/febs.14849
  • Szulczyk D, Dobrowolski MA, Roszkowski P, Bielenica A, Stefanska J, Kolinski M, et al. Design and synthesis of novel 1H-tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studies. Eur J Med Chem 2018,156:631-640. DOI: 10.1016/j.ejmech.2018.07.041
  • Bielenica A, Drzewiecka-Antonik A, Rejmak P, Stefanska J, Kolinski M, Kmiecik S, et al. Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper(II) complexes of 1,3-disubstituted thiourea ligands. J Inorg Biochem 2018,182:61-70. DOI:10.1016/j.jinorgbio.2018.01.005
  • Rakowski F, Karbowski J. Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost. PLoS Comput Biol 2017,13:e1005834. DOI:10.1371/journal.pcbi.1005834
  • Troć A, Zimnicka M, Koliński M, Danikiewicz W. Structural Elucidation of β‐Lactam Diastereoisomers through Ion Mobility Mass Spectrometry Studies and Theoretical Calculations. Journal of Mass Spectrometry 2016,51:282-290. DOI:10.1002/jms.3749
  • Pulawski W, Jamroz M, Kolinski M, Kolinski A, Kmiecik S. Coarse-grained simulations of membrane insertion and folding of small helical proteins using the CABS model. Journal of Chemical Information and Modeling 2016,56:2207-2215. DOI:10.1021/acs.jcim.6b00350
  • Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-grained protein models and their applications. Chemical reviews 2016,116:7898-7936. DOI: 10.1021/acs.chemrev.6b00163
  • Bielenica A, Kedzierska E, Kolinski M, Kmiecik S, Kolinski A, Fiorino F, et al. 5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1,3-disubstituted thiourea derivatives. Eur J Med Chem 2016,116:173-186. DOI:10.1016/j.ejmech.2016.03.073