List of Academic Publications (33)

The list contains mostly peer-reviewed articles published in journals with Impact Factor. Please click the article title to download it either as a preprint from arXiv, or from a web page of an open access publisher. If not available, feel free to drop me a line. I'll do my best to help you.

2024

33. Three epochs of nascent protein translocation through the ribosome exit tunnel

MH Kolář, H Mc Grath, FC Nepomuceno, M Černeková, submitted 2024.

32. The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability

S Codispoti, T Yamaguchi, M Makarov, VG Giacobelli, M Mašek, MH Kolář, AC Sanchez Rocha, K Fujishima, G Zanchetta, K Hlouchová, submitted 2024.

31. Sensitivity of peptide conformational dynamics in carbon nanotubes to directional mechanical forces

FC Nepomuceno, MH Kolář, 2024.

2023

30. Simulation of complex biomolecular systems: the ribosome challenge

LV Bock, S Gabrielli, MH Kolář, H Grubmüller, Annual Review of Biophysics, 2023.

2022

29. Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior

H McGrath, M Černeková, MH Kolář, Biophysical Journal, 2022, 121, 4443-4451.

28. The effect of off-center σ-hole on the atom-centered partial charges in halogenated molecules

A Leskourová, MH Kolář, Journal of Computational Chemistry, 2022, 12, 864-869.

27. Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

MH Kolář, G Nagy, J Kunkel, SM Vaiana, LV Bock, H Grubmüller, Nucleic Acids Research, 2022, gkac038.

2021

26. Kotranslační děje aneb první okamžiky života proteinu (in Czech)

MH Kolář, Chemické listy, 2021, 115, 539-578.

25. Atomistic simulations of the human proteasome inhibited by a covalent ligand

MH Kolář, LV Bock, H Grubmüller, High Performance Computing in Science & Engineering 2021, 47-57.

2020

24. Assessment of Scalar Relativistic Effects on Halogen Bonding and Sigma-Hole Properties

MH Kolář, D Suchá, M Pitoňák, The International Journal of Quantum Chemistry, 2020, e26392.

23. Antitubercular Polyhalogenated Phenothiazines and Phenoselenazine with Reduced Binding to CNS Receptors

MG Nizi, J Desantis, Y Nakatani, S Massari, MA Mazzarella, G Shetye, S Sabatini, ML Barreca, G Manfroni, T Felicetti, R Rushton-Green, K Hards, G Latacz, G Satała, A Bojarski, V Ceccheti, MH Kolář, J Handzlik, G Cook, S Franzblau, O Tabarrini, European Journal of Medicinal Chemistry, 2020, 201, 112420.

2019

Uups, there were no publications. Moving, third kid, you know...

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.

2015

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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11. Göttingen cemetery

MH Kolář, T Kubař, Vesmír, 2018, 97, 462, in Czech.

10. How are proteins born? .

MH Kolář, Vesmír, 2018, 97, 304-306, in Czech.

9. The ribosome: a stunnigly complex "nanomachine"

LV Bock, MH Kolář, AC Vaiana, H Grubmüller, MPIbpc News, 2018, April, 4-7.

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.