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

PUBLICATION/CITATION STATISTICS:

according to google scholar

PUBLICATIONS:

36

Kurcinski M, Badaczewska‐Dawid A, Kolinski M, Kolinski A, Kmiecik S: Flexible docking of peptides to proteins using CABS‐dock. Protein Science 2019.

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.

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.