Michał Koliński

e-mail address: mkolinski@imdik.pan.pl
Phone#: (+48) 22 849 93 58
Bioinformatics Laboratory,
Mossakowski Medical Research Centre
Polish Academy of Sciences
5 Pawińskiego Str.
02-106 Warsaw,
Poland


EDUCATION: 

  • Ph.D. in Biology, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Poland,  2010, Ph.D. Thesis entitled: “Modeling of structures of GPCRs and mechanisms of their activation in case of opioid receptors”
  • M.Sc. in Chemistry, University of Warsaw, Poland, 2004

PROFESSIONAL EXPERIENCE:

  • 2019-present: Head of Bioinformatics Laboratory, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
  • 2017-2018: Assistant Professor,  Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
  • 2015-2019: Assistant Professor, Bioinformatics Laboratory, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
  • 2012-2015: Senior Specialist, Bioinformatics Laboratory, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
  • 2010-2011: Postdoctoral researcher, Laboratory of Medicinal Chemistry and Neuroengineering, Medical University of Lublin, Lublin, Poland
  • 2003-2009: Research Assistant, Laboratory of Biomodelling, International Institute of Molecular and Cell Biology, Warsaw, Poland

ORCID: 0000-0003-1047-2186

PUBLICATION/CITATION STATISTICS: according to google scholar


PUBLICATIONS:

39

Badaczewska-Dawid A, Kmiecik S, Kolinski M: Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement. Briefings in Bioinformatics 2020, (accepted).

38

Dec R, Kolinski M, Kouza M, Dzwolak W: Rapid self-association of highly amyloidogenic H-fragments of insulin: Experiment and molecular dynamics simulations. International Journal of Biological Macromolecules 2020.

37

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.

36

Kurcinski M, Badaczewska‐Dawid A, Kolinski M, Kolinski A, Kmiecik S: Flexible docking of peptides to proteins using CABS‐dock. Protein Science 2020, 29(1):211-222.

35

Kmiecik S, Wabik J, Kolinski M, Kouza M, Kolinski A: Protein Dynamics Simulations Using Coarse-Grained Models. In: Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer, Cham; 2019: 61-87.

34

Dec R, Koliński M, Dzwolak W: Beyond amino acid sequence: disulfide bonds and the origins of the extreme amyloidogenic properties of insulin’s H‐fragment. The FEBS journal 2019, 286(16)3194-3205.

33

Blaszczyk M, Gront D, Kmiecik S, Kurcinski M, Kolinski M, Ciemny MP, Ziolkowska K, Panek M, Kolinski A: Protein Structure Prediction Using Coarse-Grained Models. In: Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer, Cham; 2019: 27-59.

32

Szulczyk D, Dobrowolski MA, Roszkowski P, Bielenica A, Stefańska J, Koliński M, Kmiecik S, Jóźwiak M, Wrzosek M, Olejarz W: 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. European journal of medicinal chemistry 2018, 156:631-640.

31

Bielenica A, Drzewiecka-Antonik A, Rejmak P, Stefańska J, Koliński M, Kmiecik S, Lesyng B, Włodarczyk M, Pietrzyk P, Struga M: Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper (II) complexes of 1, 3-disubstituted thiourea ligands. Journal of inorganic biochemistry 2018, 182:61-70.

30

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(4):282-290.

29

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(11):2207-2215.

28

Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A: Coarse-grained protein models and their applications. Chemical reviews 2016, 116(14):7898-7936.

27

Bielenica A, Kędzierska E, Koliński M, Kmiecik S, Koliński A, Fiorino F, Severino B, Magli E, Corvino A, Rossi I: 5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1, 3-disubstituted thiourea derivatives. European journal of medicinal chemistry 2016, 116:173-186.

26

Yuan S, Palczewski K, Peng Q, Kolinski M, Vogel H, Filipek S: The Mechanism of Ligand‐Induced Activation or Inhibition of μ‐and κ‐Opioid Receptors. Angewandte Chemie International Edition 2015, 54(26):7560-7563.

25

Horwacik I, Golik P, Grudnik P, Kolinski M, Zdzalik M, Rokita H, Dubin G: Structural basis of GD2 ganglioside and mimetic peptide recognition by 14G2a antibody. Molecular & Cellular Proteomics 2015, 14(10):2577-2590.

24

Zimnicka M, Troć A, Ceborska M, Jakubczak M, Koliński M, Danikiewicz W: Structural elucidation of specific noncovalent association of folic acid with native cyclodextrins using an ion mobility mass spectrometry and theoretical approach. Analytical chemistry 2014, 86(9):4249-4255.

23

Lazarova T, Mlynarczyk K, Filipek S, Kolinski M, Wassenaar TA, Querol E, Renugopalakrishnan V, Viswanathan S, Padrós E: The effect of triple glutamic mutations E9Q/E194Q/E204Q on the structural stability of bacteriorhodopsin. The FEBS journal 2014, 281(4):1181-1195.

22

Kmiecik S, Wabik J, Kolinski M, Kouza M, Kolinski A: Coarse-grained modeling of protein dynamics. In: Computational methods to study the structure and dynamics of biomolecules and biomolecular processes. Springer, Berlin, Heidelberg; 2014: 55-79.

21

Kmiecik S, Jamroz M, Kolinski M: Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors. Biophysical Journal 2014:2408–2416.

20

Plazinska A, Kolinski M, Wainer IW, Jozwiak K: Molecular interactions between fenoterol stereoisomers and derivatives and the β 2-adrenergic receptor binding site studied by docking and molecular dynamics simulations. Journal of molecular modeling 2013, 19(11):4919-4930.

19

Sosnowski TR, Koliński M, Gradoń L: Alteration of surface properties of dipalmitoyl phosphatidylcholine by benzo [a] pyrene: a model of pulmonary effects of diesel exhaust inhalation. Journal of biomedical nanotechnology 2012, 8(5):818-825.

18

Kolinski M, Plazinska A, Jozwiak K: Recent progress in understanding of structure, ligand interactions and the mechanism of activation of the β 2-adrenergic receptor. Current medicinal chemistry 2012, 19(8):1155-1163.

17

Dawid A, Kolinski M, Koliński A, Kmiecik S: Modelowanie Molekularne Białek Błonowych (Molecular Modeling of Membrane Proteins). Na pograniczu chemii i biologii (At the Treshold of Chemistry and Biology) vol XXVIII, H Koroniak, J Barciszewski eds, Wydawnictwo Naukowe UAM, Poznań 2012.

16

Sosnowski TR, Koliński M, Gradoń L: Interactions of benzo [a] pyrene and diesel exhaust particulate matter with the lung surfactant system. Annals of occupational hygiene 2011, 55(3):329-338.

15

Latek D, Kolinski M, Ghoshdastider U, Debinski A, Bombolewski R, Plazinska A, Jozwiak K, Filipek S: Modeling of ligand binding to G protein coupled receptors: cannabinoid CB 1, CB 2 and adrenergic β 2 AR. Journal of molecular modeling 2011, 17(9):2353-2366.

14

Audette GF, Lombardo S, Dudzik J, Arruda TM, Kolinski M, Filipek S, Mukerjee S, Kannan AM, Thavasi V, Ramakrishna S: Protein hot spots at bio-nano interfaces. Materials Today 2011, 14(7-8):360-365.

13

Sosnowski T, Koliński M, Gradoń L: Wpływ benzo [a] pirenu na własności fosfolipidów surfaktantu płucnego: modelowa analiza toksyczności spalin silników Diesla. Inżynieria i Aparatura Chemiczna 2010(2):115-116.

12

Sobhanifar S, Schneider B, Löhr F, Gottstein D, Ikeya T, Mlynarczyk K, Pulawski W, Ghoshdastider U, Kolinski M, Filipek S: Structural investigation of the C-terminal catalytic fragment of presenilin 1. Proceedings of the National Academy of Sciences 2010, 107(21):9644-9649.

11

Kolinski M, Filipek S: Study of a structurally similar kappa opioid receptor agonist and antagonist pair by molecular dynamics simulations. Journal of molecular modeling 2010, 16(10):1567-1576.

10

Thavasi V, Lazarova T, Filipek S, Kolinski M, Querol E, Kumar A, Ramakrishna S, Padrós E, Renugopalakrishnan V: Study on the feasibility of bacteriorhodopsin as bio-photosensitizer in excitonic solar cell: a first report. Journal of nanoscience and nanotechnology 2009, 9(3):1679-1687.

9

Kolinski M, Filipek S: Studies of the activation steps concurrent to ligand binding in DOR and KOR opioid receptors based on molecular dynamics simulations. TOSBJ 2009, 3:51-63.

8

Jaworski JS, Kosson A, Filipek S, Kuck D: Properties of Radical Anions of Triptindanones and Indanones: Electronic Communication and Stability of Ion Pairs Containing Lithium Cations. The Journal of Physical Chemistry C 2009, 113(17):7436-7442.

7

Austermann J, Nazmi AR, Heil A, Fritz G, Kolinski M, Filipek S, Gerke V: Generation and characterization of a novel, permanently active S100P mutant. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 2009, 1793(6):1078-1085.

6

Kolinski M, Filipek S: Molecular dynamics of mu opioid receptor complexes with agonists and antagonists. TOSBJ 2008, 2:8-20.

5

Bhatia P, Kolinski M, Moaddel R, Jozwiak K, Wainer I: Determination and modelling of stereoselective interactions of ligands with drug transporters: a key dimension in the understanding of drug disposition. Xenobiotica 2008, 38(7-8):656-675.

4

Park PS-H, Sapra KT, Koliński M, Filipek S, Palczewski K, Muller DJ: Stabilizing effect of Zn2+ in native bovine rhodopsin. Journal of Biological Chemistry 2007, 282(15):11377-11385.

3

Krzysko K, Kolinski M, Filipek S: Molecular modelling of the complex of oligomeric rhodopsin and its G protein. Journal of Physics: Condensed Matter 2007, 19(28):285204.

2

Jaworski JS, Cembor M, Koliński M: Electrostatic model of bond dissociation energies in polyhalogen methanes. Journal of physical organic chemistry 2006, 19(4):276-280.

1

Filipek S, Kolinski M, Siadkowska E, Kolczewska M: Modeling of opioid receptors and ligand binding. European Journal of Biochemistry Supplement 2004, 271.