List of Peer-Reviewed Scientific Publications (22)

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2018

22. Molecular Simulations of the Ribosome and Associated Translation Factors

LV Bock, MH Kolář, H Grubmüller, Current Opinion in Structural Biology, 2018, 49, 27-35.

2017

21. Halogen Bonding in Nucleic Acid Complexes

MH Kolář, O Tabarrini, The Journal of Medicinal Chemistry, 2017, 60, 8681-8690.

20. Reaction Path Averaging: Characterizing Structural Response of the DNA Double Helix upon Electron Transfer

MH Kolář, T Kubař, The Journal of Physical Chemistry B, 2017, 121, 1520-1532.

2016

19. Computer Modeling of Halogen Bonds and Other sigma-Hole Interactions

MH Kolář, P Hobza, Chemical Reviews, 2016, 116, 5155-5187.

18. Polar Flattening and the Strength of Halogen Bonding

R Sedlák, MH Kolář, P Hobza, The Journal of Chemical Theory and Computation, 2015, 11, 4727-4732

17. Enzymatic characterization and structural modeling of human aldo-keto reductase 1B15: A novel retinaldehyde reductase

J Gimenez-Dejoz, MH Kolář, FX Ruiz, I. Crespo, A Cousido-Siah, A Podjarny, O Barski, J Fanfrlík, X Parés, J Farrés, S Porte, PLoS ONE, 2015, 10: e0134506

16. The effect of halogen-to-hydrogen bond substitution on human aldose reductase inhibition

J Fanfrlík, FX Ruiz, A Kadlčíková, J Řezáč, A Cousido-Siah, A Mitschler, S Haldar, M Lepšík, MH Kolář, P Majer, A Podjarny, P Hobza, ACS Chemical Biology, 2015, 10, 1637-1642

15. The characteristics of sigma-hole and the nature of a halogen bond

MH Kolář, P Deepa, H Ajani, A Pecina, P Hobza, Topics in Current Chemistry, 2015, 359, 1-25

2014

14. Statistical Analysis of sigma-holes: A novel complementary view on halogen bonding

MH Kolář, P Carloni, P Hobza, Physical Chemistry Chemical Physics, 2014, 16, 19111-19114

13. The strength and directionality of a halogen bond is co-determined by the magnitude and size of the sigma-hole

M Kolář, J Hostaš, P Hobza, Physical Chemistry Chemical Physics, 2014, 16, 9987-9996

< 2013 (undergraduate)

12. The modulation of aldose reductase inhibition by halogen bond tuning

J Fanfrlík, M Kolář, M Kamlar, D Hurný, FX Ruiz, A Cousido-Siah, A Mitschler, J Řezáč, E. Munusamy, M Lepšík, P Matějíček, J Veselý, A Podjarny, P Hobza, ACS Chemical Biology, 2013, 8, 2484-2492

11. The semiempirical quantum mechanical scoring function for in-silico drug design

M Lepšík, J Řezáč, M Kolář, A Pecina, P Hobza, J Fanfrlík, ChemPlusChem, 2013, 78, 921-931

10. Assessing the accuracy and performance of implicit solvent models for drug molecules: conformational ensemble approaches

M Kolář, J Fanfrlík, M Lepšík, F Forti, FJ Luque, P Hobza, The Journal of Physical Chemistry B, 2013, 117 (19), 5950-5962

9. The differences in the sublimation energy of benzene and hexahalogenbenzenes are caused by dispersion energy

J Trnka, R Sedlák, M Kolář, P Hobza, The Journal of Physical Chemistry A, 2013, 117 (20), 4331-4337

8. Plugging the explicit sigma-holes in molecular docking

M Kolář, P Hobza, AK Bronowska, Chemical Communications, 2013, 49 (10), 981-983

7. Adsorption of organic electron acceptors on graphene-like molecules: quantum chemical and molecular mechanical study

S Haldar, M Kolář, P Sedlák, P Hobza, The Journal of Physical Chemistry C, 2012, 116 (48), 25328-25336

6. On extension of the current biomolecular empirical force field for the description of halogen bonds

M Kolář, P Hobza, The Journal of Chemical Theory and Computation, 2012, 8, 1325-1333

5. On the role of London dispersion forces in biomolecular structure determination

M Kolář, T Kubař, P Hobza, The Journal of Physical Chemistry B, 2011, 115(24), 8038-8046

4. Ligand conformational and solvation/desolvation free energy in protein-ligand complex formation

M Kolář, J Fanfrlík, P Hobza, The Journal of Physical Chemistry B, 2011, 115(16), 4718-4724

3. Sequence-dependent configurational entropy change of DNA upon intercalation

M Kolář, T Kubař, P Hobza, The Journal of Physical Chemistry B, 2010, 114(42), 13446-13454

2. On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes

M Kolář, K Berka, P Jurečka, P Hobza, ChemPhysChem, 2010, 11, 2399-2408

1. Accurate theoretical determination of the structure of aromatic complexes is complicated: The phenol dimer and phenol...methanol cases

M Kolář, P Hobza, The Journal of Physical Chemistry A, 2007, 111(26), 5851-5854

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List of Popular Science Articles (8)

8. Stories according to a mathematical template

MH Kolář, Vesmír, 2017, 96, 482-483, in Czech.

7. Beyond the borders of the current theoretical biophysics

MH Kolář, Vesmír, 2017, 96, 76-77, in Czech.

6. Crystallography without crystals

M Kolář, Vesmír, 2014, 93, 568-570, in Czech.

5. Classical or quantum atom?

M Kolář, Vesmír, 2013, 92, 706-707, in Czech.

4. Computer alchemy

M Kolář, Vesmír, 2013, 92, 571-573, in Czech.

3. Evolution of protein folding

M Kolář, Vesmír, 2013, 92, 263-264, in Czech.

2. Is it really hydrogen bonding what keeps DNA strands together?

M Kolář, P Hobza, Vesmír, 2013, 92, 140-141, in Czech.

1. Halogen bond, or muddled charges as a hope for current medicine

M Kolář, Vesmír, 2012, 91, 522-523, in Czech.