Hawash M, Qneibi M, Natsheh H, Mohammed NH, Hamda LA, Kumar A, Olech B, Dominiak PM , Bdir S, Bdair M
Evaluating the Neuroprotective Potential of Novel Benzodioxole Derivatives in Parkinson’s Disease via AMPA Receptor Modulation
ACS Chem. Neurosci. 2024, XXXX, XXX, XXX-XXX, Published: 2024
[DOI: 10.1021/acschemneuro.4c00163]
Olech B, Brázda P, Palatinus L, Dominiak PM
Dynamical refinement with multipolar electron scattering factors
IUCrJ, Volume 11, part 3, 309-324, Published: 2024
[DOI: 10.1107/S2052252524001763]
Hawash M, Abdallah S, Abudayyak M, Melhem Y, Shamat MA, Aghbar M, Çapan I, Abualhasan M, Kumar A, Kamiński M, Góral T, Dominiak PM, Sobuh S
Exploration of isoxazole analogs: Synthesis, COX inhibition, anticancer screening, 3D multicellular tumor spheroids, and molecular modeling
European Journal of Medicinal Chemistry, Volume 271, 116397, Published: 2024
[DOI: 10.1016/j.ejmech.2024.116397]
Bick T, Dominiak PM, Wendler P
Exploiting the full potential of cryo-EM maps
BBA Advances, Volume 5, 100113, Published: 2024
[DOI: 10.1016/j.bbadva.2024.100113]


Hawash M, Al-Smadi D, Kumar A, Olech B, Dominiak PM, Jaradat, N, Antari S, Mohammed S, Nasasrh A, Abualhasan M, Musa A, Suboh S, Çapan İ, Qneibi M, Natsheh H
Characterization and Investigation of Novel Benzodioxol Derivatives as Antidiabetic Agents: An In Vitro and In Vivo Study in an Animal Model
Biomolecules, 13, 1486, Published: 2023
[DOI: 10.3390/biom1310148]
Jha KK, Kleemiss F, Chodkiewicz ML, Dominiak PM
Aspherical Atom Refinements on X-Ray Data of Diverse Structures Including Disordered and Covalent Organic Framework Systems: A Time–Accuracy Trade-Off
J. Appl. Crystallogr., 56 (1), 116–127, Published: 2023
[DOI: 10.1107/S1600576722010883]
Landeros-Rivera B, Ramírez-Palma D, Cortes-Guzman F, Dominiak PM, Contreras García J
How do density functionals affect the Hirshfeld atom refinement?
Phys. Chem. Chem. Phys., 25, 12702, Published: 2023
[DOI: 10.1039/D2CP04098K ]


Budniak UA, Karolak NK, Kulik M, Młynarczyk K, Górna MW, Dominiak PM
The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method
J. Phys. Chem. B., 126, 45, 9152–9167, Published: 2022
Kulik M, Dominiak PM
Electron density is not spherical: the many applications of the transferable aspherical atom model
Computational and Structural Biotechnology Journal, 20, 6237-6243, Published: 2022
[DOI: 10.1016/j.csbj.2022.10.018]
Bojarowski SA, Gruza B, Trzybiński D, Kamiński R, Hoser AA, Kumar P, Woźniak K, Dominiak PM
New refinement strategies for a pseudoatom databank – toward rapid electrostatic interaction energy estimations
Acta Cryst. B78, 823-834, Published: 2022
[DOI: 10.1107/S2052520622008800]
Rybicka PM, Kulik M, Chodkiewicz ML, Dominiak PM
Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis
J. Chem. Inf. Model., 62 (16), 3766–3783, Published: 2022
[DOI: 10.1021/acs.jcim.2c00145]Jha KK, Gruza B, Sypko A, Kumar P, Chodkiewicz ML, Dominiak PM
Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB
J. Chem. Inf. Model., 62 (16), 3752–3765, Published: 2022
[DOI: 10.1021/acs.jcim.2c00144]
Kulik M, Chodkiewicz ML, Dominiak PM
Theoretical 3D ED electrostatic potential density maps of proteins modeled with multipolar pseudoatom data bank
Acta Crystallographica Section D Structural Biology, 78 (8), 1010–1020, Published: 2022
[DOI: 10.1107/S2059798322005836]
Ziemniak M, Pawlędzio S, Zawadzka-Kaźmierczuk A, Dominiak PM, Trzybiński D, Koźmiński W, Zieliński R, Fokt I, Priebe W, Woźniak K, Pająk B
X-Ray Wavefunction Refinement and Comprehensive Structural Studies on Bromo-Substituted Analogues of 2-Deoxy-d-Glucose in Solid State and Solution
RSC Adv., 12 (14), 8345–8360, Published: 2022
[DOI: 10.1039/d1ra08312k]


Landeros-Rivera B, Contreras-García J, Dominiak PM
The influence of refinement strategies on the wavefunctions derived from an experiment
Acta Crystallographica Section B 77, 715-727, Published: 2021
[DOI: 10.1107/S2052520621008258]
Kumar P, Dominiak PM
Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease
Molecules 26, 3872-3887, Published: 2021
[DOI: 10.3390/molecules26133872]
Jha KK, Gruza B, Chodkiewicz ML, Jelsch Ch, Dominiak PM
Refinements on electron diffraction data of β-glycine in MoPro: A quest for improved structure model
Journal of Applied Crystallography 54, 1234-1243, Published: 2021
[DOI: 10.1107/S160057672100580X]
Cabaj MK, Dominiak PM
Phase transition of hypoxanthinium nitrate monohydrate
Crystal Growth and Design 21, 424-435, Published: 2021
[DOI: 10.1021/acs.cgd.0c01252]


Brunner JS, Vogel A, Lercher A, Caldera M, Korosec A, Pühringer M, Hofmann M, Hajto A, Kieler M, Garrido LQ, Kerndl M, Kuttke M, Mesteri I, Górna MW, Kulik M, Dominiak PM, Brandon AE, Estevez E, Egan CL, Gruber F, Schweiger M, Menche J, Bergthaler A, Weichhart T, Klavins K, Febbraio MA, Sharif O, Schabbauer G
The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages
Nature Metabolism, Published: 2020
[DOI: 10.1038/s42255-020-00311-5]
Sanjuan-Szklarz FW, Woińska M, Domagała S, Dominiak PM, Grabowsky S, Jayatilaka D, Gutmannd M, Woźniak K
On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model
IUCrJ, 7, 920-933, Published: 2020
[DOI: /10.1107/S2052252520010441]
Cabaj MK, Dominiak PM
Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals
Nucleic Acids Research 48, 8302-8319, Published: 2020
[DOI: 10.1093/nar/gkaa629]
Jha KK, Gruza B, Kumar P, Chodkiewicz ML, Dominiak PM
TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data
Acta Crystallographica Section B 76, 296-306, Published: 2020
[DOI: /10.1107/S2052520620002917]
Gruza B, Chodkiewicz ML, Krzeszczakowska J, Dominiak PM
Refinement of organic crystal structures with multipolar electron scattering factors
Acta Crystallographica Section A 76, 92-109, Published: 2020
[DOI: 10.1107/S2053273319015304]


Kumar P, Cabaj MK, Dominiak PM
Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions
Crystals 9, 688-705, Published: 2019
[DOI: 10.3390/cryst9120668 ]
Cabaj MK, Gajda R, Hoser A, Makal A, Dominiak PM
Differences and similarities among hypoxanthinium nitrate hydrate structures
Acta Crystallographica Section C 75, 1036-1044, Published: 2019
[DOI: 10.1107/S2053229619008702]
Kumar P, Gruza B, Bojarowski SA, Dominiak PM
Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies
Acta Crystallographica Section A 75, 398-408, Published: 2019
[DOI: 10.1107/S2053273319000482]


Bojarowski SA, Kumar P, Wandtke CM, Bittrich B, Dominiak PM
Universal Method for Electrostatic Interaction Energies Estimation with Charge Penetration and Easily Attainable Point Charges
Journal of Chemical Theory and Computation 14, 12, 6336–6345; Published: 2018
[DOI: 10.1021/acs.jctc.8b00781]
Genoni A, Bucinsky L, Claiser N, Contreras-Garcia J, Dittrich B, Dominiak PM, et al.
Quantum Crystallography: Current Developments and Future Perspectives
Chemistry – A European Journal 24, 43, 10881-10905; Published: 2018
[DOI: 10.1002/chem.201705952]

Kumar P, Cabaj MK, Pazio A, Dominiak PM
Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions
IUCrJ 5, 449-469; Published: 2018
[DOI: 10.1107/S2052252518006346]
Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM
DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs
Journal of Applied Crystallography 51, 193-199, Published: 2018
[DOI: 10.1107/S1600576717015825]
Budniak UA, Dominiak PM
Molecular tapes in the structure of isoguaninium chloride
Acta Crystallographica Section C 74, 108-112, Published: 2018
[DOI: 10.1107/S2053229617017685]


Woinska M, Jayatilaka D, Dittrich B, Flaig R, Luger P, Wozniak K, Dominiak PM, Grabowsky S
Validation of X-ray Wavefunction Refinement
ChemPhysChem 18, 3334-3351, Published: 2017
[DOI: 10.1002/cphc.201700810]

Jarzembska KN, Slepokura K, Kaminski R, Gutmann MJ, Dominiak PM, Wozniak K
Multi-temperature study of potassium uridine-5 ‘ monophosphate: electron density distribution and anharmonic motion modelling
Acta Crystallographica Section B 73, 550-564, Published: 2017
[DOI: 10.1107/S2052520617005534]
Bojarowski SA, Kumar P, Dominiak PM
Interplay of point multipole moments and charge penetration for intermolecular electrostatic interaction energies from the University at Buffalo pseudoatom databank model of electron density
Acta Crystallographica Section B 73, 598-609, Published: 2017
[DOI: 10.1107/S2052520617005510]


Bojarowski SA, Kumar P, Dominiak PM
A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation
ChemPhysChem 17, 2455-2460, Published: 2016
[DOI: 10.1002/cphc.201600390]
Woinska M, Grabowsky S, Dominiak PM, Wozniak K, Jayatilaka D
Hydrogen atoms can be located accurately and precisely by x-ray crystallography
Science Advances 2, Published: 2016
[DOI: 10.1126/sciadv.1600192]


Adamczyk-Wozniak A, Cabaj MK, Dominiak PM, Gajowiec P, Gierczyk B, Lipok J, Popenda L, Schroeder G, Tomecka E, Urbanski P, Wieczorek D, Sporzynski A
The influence of fluorine position on the properties of fluorobenzoxaboroles
Bioorganic Chemistry 60, 130-135, Published: 2015
[DOI: 10.1016/j.bioorg.2015.05.004]
Kulik M, Goral AM, Jasinski M, Dominiak PM, Trylska J
Electrostatic Interactions in Aminoglycoside-RNA Complexes
Biophysical Journal 108, 655-665, Published: 2015
[DOI: 10.1016/j.bpj.2014.12.020]


Woinska M, Jayatilaka D, Spackman MA, Edwards AJ, Dominiak PM, Wozniak K, Nishibori E, Sugimoto K, Grabowsky S
Hirshfeld atom refinement for modelling strong hydrogen bonds
Acta Crystallographica Section A 70, 483-498, Published: 2014
[DOI: 10.1107/S2053273314012443]
Malinska M, Jarzembska KN, Goral AM, Kutner A, Wozniak K, Dominiak PM
Sunitinib: from charge-density studies to interaction with proteins
Acta Crystallographica Section D 70, 1257-1270, Published: 2014
[DOI: 10.1107/S1399004714002351]
Kumar P, Bojarowski SA, Jarzembska KN, Domagala S, Vanommeslaeghe K, MacKerell AD, Dominiak PM
A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers
Journal of Chemical Theory and Computation 10, 1652-1664, Published: 2014
[DOI: 10.1021/ct4011129]
Dominiak PM
The importance and examples of application of aspherical pseudoatom databanks in small-molecule crystallography and their potential use in makromolecular crystallography
Wiadomości Chemiczne 68, 429–455, Published: 2014
[YADDA: bwmeta1.element.baztech-8d225708-fbd7-453f-8ac1-9645b48628d9], paper in Polish


Jarzembska KN, Kaminski R, Wenger E, Lecomte C, Dominiak PM
Interplay between Charge Density Distribution, Crystal Structure Energetic Features, and Crystal Morphology of 6-Methyl-2-thiouracil
Journal of Physical Chemistry C 117, 7764-7775, Published: 2013
[DOI: 10.1021/jp312158m]
Woinska M, Dominiak PM
Transferability of Atomic Multipoles in Amino Acids and Peptides for Various Density Partitions
Journal of Physical Chemistry A 117, 1535-1547, Published: 2013
[DOI: 10.1021/jp204010v]
Wesela-Bauman G, Boinski T, Dominiak P, Hajmowicz H, Synoradzki L, Wierzbicki M, Wolinski B, Wozniak K, Zawada K
Tartaric acid and its O-acyl derivatives. 7. Crystal structure of O-p-anisoyl-D-tartaric acid and its dimethylammonium salt trihydrate
Journal of Structural Chemistry 54, 155-158, Published: 2013
[DOI: 10.1134/S0022476613010228]
Jarzembska KN, Goral AM, Gajda R, Dominiak PM
Hoogsteen-Watson-Crick 9-Methyladenine:1-Methylthymine Complex: Charge Density Study in the Context of Crystal Engineering and Nucleic Acid Base Pairing
Crystal Growth and Design 13, 239-254, Published: 2013
[DOI: 10.1021/cg301393e]


Bak JM, Czyznikowska Z, Dominiak PM
Is it possible to derive quantitative information on polarization of electron density from the multipolar model?
Acta Crystallographica Section A 68, 705-714, Published: 2012
[DOI: 10.1107/S010876731203317X]
Jarzembska KN, Kubsik M, Kaminski R, Wozniak K, Dominiak PM
From a Single Molecule to Molecular Crystal Architectures: Structural and Energetic Studies of Selected Uracil Derivatives
Crystal Growth and Design 12, 2508-2524, Published: 2012
[DOI: 10.1021/cg300129z]
Jarzembska KN, Dominiak PM
New version of the theoretical databank of transferable aspherical pseudoatoms, UBDB2011-towards nucleic acid modelling
Acta Crystallographica Section A 68, 139-147, Published: 2012
[DOI: 10.1107/S0108767311042176]


Bak JM, Domagala S, Hubschle C, Jelsch C, Dittrich B, Dominiak PM
Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases
Acta Crystallographica Section A 67, 141-153, Published: 2011
[DOI: 10.1107/S0108767310049731]


Czyznikowska Z, Gora RW, Zalesny R, Lipkowski P, Jarzembska KN, Dominiak PM, Leszczynski J
Structural Variability and the Nature of Intermolecular Interactions in Watson-Crick B-DNA Base Pairs
Journal of Physical Chemistry B 114, 9629-9644, Published: 2010
[DOI: 10.1021/jp101258q]


Bak JM, Dominiak PM, Wilson CC, Wozniak K
Experimental charge-density study of paracetamol – multipole refinement in the presence of a disordered methyl group
Acta Crystallographica Section A 65, 490-500, Published: 2009
[DOI: 10.1107/S0108767309031729]
Dominiak PM, Volkov A, Dominiak AP, Jarzembska KN, Coppens P
Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme-substrate complex: influenza neuraminidase inhibition
Acta Crystallographica Section D 65, 485-499, Published: 2009
[DOI: 10.1107/S0907444909009433]