B. Niklas, J. Rydzewski, Bruno Lapied, W. Nowak "Toward Overcoming Pyrethroid Resistance in Mosquito Control: The Role of Sodium Channel Blocker Insecticides" Int. J. Mol. Sci.24(12) (2023), 10334 DOI: https://doi.org/10.3390/ijms241210334
2022
J. Rydzewski, K. Walczewska-Szewc, S. Czach, W. Nowak, Kuczera Krzysztof "Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome" J. Phys. Chem. B126 (2022), 2647-2657 DOI: 10.1021/acs.jpcb.2c00131
2021
B. Niklas, Milena Jankowska, Dalia Gordon, László Béress, Maria Stankiewicz, W. Nowak " Interactions of Sea Anemone Toxins with Insect Sodium Channel—Insights from Electrophysiology and Molecular Docking Studies " Molecules26 (5) (2021), 1302-1324 DOI: : https://www.mdpi.com/1420-3049/26/5/1302
K. Walczewska-Szewc, W. Nowak "Photo-Switchable Sulfonylureas Binding to ATP-Sensitive Potassium Channel Reveal the Mechanism of Light-Controlled Insulin Release" J. Phys. Chem. B125, 48 (2021), 13111-13121 DOI: 10.1021/acs.jpcb.1c07292
2020
Jakub Dąbrowski, W. Nowak, Arkadiusz Ptak "How strong are hydrogen bonds in the peptide model?" Phys. Chem. Chem. Phys.22 (2020), 1392-1399 DOI: https://doi.org/10.1039/C9CP05564A
Eléonore Moreau, K. Mikulska-Rumińska, Mathilde Goulu, Stéphane Perrier, Caroline Deshayes, Maria Stankiewicz, Véronique Apaire-Marchais, W. Nowak, Bruno Lapied "Orthosteric muscarinic receptor activation by the insect repellent IR3535 opens new prospects in insecticide-based vector control" Sci. Rep.10 (2020), 1-15 DOI: 10.1038/s41598-020-63957-x
K. Walczewska-Szewc, W. Nowak "Structural Determinants of Insulin Release: Disordered N-Terminal Tail of Kir6.2 Affects Potassium Channel Dynamics Through Interactions With Sulfonylurea Binding Region in a SUR1 Partner" J. Phys. Chem. B 124, 29 (2020), 6198-6211 DOI: 10.1021/acs.jpcb.0c02720
2019
Marta Stawczyk‐Macieja , Katarzyna Wertheim‐Tysarowska , Rafał Jakubowski , Aneta Szczerkowska‐Dobosz , Magdalena Krygier , Aleksandra Wilkowska , Justyna Sawicka , W. Nowak, Jerzy Bal , Roman Nowicki "A novel de novo mutation p.Ala428Asp in KRT5 gene as a cause of localized epidermolysis bullosa simplex." EXP DERMATOL28(10) (2019), 1131-1134 DOI: 10.1111/exd.13788
K. Mikulska-Rumińska, J. Strzelecki, W. Nowak "Dynamics, nanomechanics and signal transduction in reelin repeats" Sci. Rep.9 (2019), 1-13
Juan Francisco Carrascoza Mayén, J. Rydzewski, Natalia Szostak, Jacek Blazewicz, W. Nowak "Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations" Life9 (2019), 46-54 DOI: doi:10.3390/life9020046
K. Walczewska-Szewc, W. Nowak "Spacial models of malfunctioned protein complexes help to elucidate signal transduction critical for insulin release" Biosystems177 (2019), 48-55 DOI: https://doi.org/10.1016/j.biosystems.2018.11.001
Renata Gadzała-Kopciuch, Katarzyna Kwaśniewska, Agnieszka Ludwiczak, Piotr Skrzyniarz, R. Jakubowski, W. Nowak, Andrzej Wojtczak, Bogusław Buszewski "Towards A New Approach for the Description of Cyclo–2,4-Dihydroxybenzoate, A Substance Which Effectively Mimics Zearalenone in Imprinted Polymers Designed for Analyzing Selected Mycotoxins in Urine" Int. J. Mol. Sci.20(7) (2019), 1588-1610 DOI: https://doi.org/10.3390/ijms20071588
2018
Anna Kutkowska-Kaźmierczak, Małgorzata Rydzanicz, Aleksander Chlebowski, Kamila Kłosowska-Kosicka, Adriana Mika, Jakub Gruchota, Elżbieta Jurkiewicz, Cezary Kowalewski, Agnieszka Pollak, Teresa Joanna Stradomska, Tomasz Kmieć, R. Jakubowski, Piotr Gasperowicz, Anna Walczak, Dariusz Śladowski, Ewa Jankowska-Steifer, Lech Korniszewski, Joanna Kosińska, Ewa Obersztyn, W. Nowak, Tomasz Śledziński, Andrzej Dziembowski, Rafał Płoski, 22 "Dominant ELOVL1 mutation causes neurological disorder with ichthyotic keratoderma, spasticity, hypomyelination and dysmorphic features" J. Med. Genet.55(6) (2018), 408-414 DOI: http://dx.doi.org/10.1136/jmedgenet-2017-105172
J. Rydzewski, dr inż. Rafał Jakubowski, W. Nowak, prof. Helmut Grubmueller "Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways" J. Chem. Theory Comput. 14 (6) (2018), 2843- 2851 DOI: DOI: 10.1021/acs.jctc.8b00173
J. Rydzewski, W. Nowak "Photoinduced Transport in an H64Q Neuroglobin Antidote for Carbon Monoxide Poisoning" J. Chem. Phys.148(11) (2018), 115101- DOI: https://doi.org/10.1063/1.5013659
2017
Katarzyna Roszek, Noemi Makowska, Joanna Czarnecka, Dorota Porowińska, M. Dąbrowski, Justyna Danielewska, W. Nowak "Canine Adipose‐Derived Stem Cells: Purinergic Characterization and Neurogenic Potential for Therapeutic Applications" J. Cell. Biochem. 118(1) (2017), 58-65 DOI: 10.1002/jcb.25610
J. Rydzewski, W. Nowak "Ligand diffusion in proteins via enhanced sampling in molecular dynamics" Phys. Life Rev. 22-23 (2017), 58- 74 DOI: 10.1016/j.plrev.2017.03.003
K. Mikulska-Rumińska, A. J. Kulik, C. Benadiba, I. Bahar, G. Dietler, W. Nowak "Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD" Sci. Rep.7 (2017), 1-11 DOI: 10.1038/s41598-017-09482
J. Rydzewski, W. Nowak "Rare-event sampling in ligand diffusion: Reply to comments on “Ligand diffusion in proteins via enhanced sampling in molecular dynamics”" Phys. Life Rev.22-23 (2017), 82- 85 DOI: 10.1016/j.plrev.2017.08.011
J. Rydzewski, R. Jakubowski, prof. Giuseppe Nicosia, W. Nowak "Conformational sampling of a biomolecular rugged energy landscape" IEEE/ACM Trans. Comput. Biol. (2016), - DOI: 10.1109/TCBB.2016.2634008
J. Rydzewski, W. Nowak "Machine learning based dimensionality reduction facilitates ligand diffusion paths assessment: a case of cytochrome P450cam" J. Chem. Theory Comput. (2016), - DOI: 10.1021/acs.jctc.6b00212
A. Gogolińska, R. Jakubowski, W. Nowak "Petri nets formalism facilitates analysis of complex biomolecular structural data" Rairo-Oper. Res. 50 (2016), 401-411 DOI: http://dx.doi.org/10.1051/ro/2015043
2015
M. Dąbrowski, Katarzyna Roszek, J. Strzelecki, Maria Stankiewicz, W. Nowak "Afm Monitoring of Elasticity Changes Accompanying Differentiation Towards Neural Cells" Biophys. J. Suppl. 108 (2015), 169a-169a DOI: http://dx.doi.org/10.1016/j.bpj.2014.11.934
J. Rydzewski, R. Jakubowski, W. Nowak "Entropic measure to prevent energy over-minimization in molecular dynamics simulations" J. Chem. Phys.143(19) (2015), 171103 DOI: 10.1063/1.4935370
J. Rydzewski, W. Nowak, Giussepe Nicosia "Inferring pathological states in cortical neuron microcircuits" J. Theor. Biol.386 (2015), 34-43 DOI: doi:10.1016/j.jtbi.2015.09.004
J. Rydzewski, W. Nowak "Memetic algorithms for ligand expulsion from protein cavities" J. Chem. Phys.143(12) (2015), 124101- DOI: 10.1063/1.4931181
J. Rydzewski, Wojciech Strzałka, W. Nowak "Nanomechanics of PCNA: A protein-made DNA sliding clamp" Chem. Phys. Lett.634 (2015), 236-242 DOI: doi:10.1016/j.cplett.2015.06.027
R. Jakubowski, J. Rydzewski, W. Nowak "On the role of metal ions in synaptic proteins assembly" Protein Sci. 24 (2015), 161-162
Andrzej J. Kulik, Małgorzata Lekka, Kyumin Lee, Grazyna Pyka-Fościak, W. Nowak "Probing fibronectin–antibody interactions using AFM force spectroscopy and lateral force microscopy" BEILSTEIN J NANOTECH6 (2015), 1164-1175 DOI: doi:10.3762/bjnano.6.118
Aly Abd-Ella, Maria Stankiewicz, K. Mikulska-Rumińska, W. Nowak, Cédric Pennetier, Mathilde Goulu, Carole Fruchart-Gaillard, Patricia Licznar, Véronique Apaire-Marchais, Olivier List, Vincent Corbel, Denis Servent, Bruno Lapied "The Repellent DEET Potentiates Carbamate Effects via Insect Muscarinic Receptor Interactions: An Alternative Strategy to Control Insect Vector-Borne Diseases" PLOS ONE10(5) (2015), e0126406-+20 DOI: DOI:10.1371/journal.pone.0126406
2014
K. Kubiak-Ossowska, Mulheran Paul, W. Nowak "Fibronectin Module FNIII9 Adsorption at Contrasting Solid Model Surfaces Studied by Atomistic Molecular Dynamics" J. Phys. Chem. Bxx (2014), yy-zz DOI: 10.1021/jp5020077
J. Strzelecki, Ł. Pepłowski, Lenartowski Robert, W. Nowak, A. Balter "Mechanical transition in a highly stretched and torsionally constrained DNA" Phys. Rev. E.89 (2014), 020701-1-020701-5 DOI: 10.1103/PhysRevE.89.020701
K. Mikulska-Rumińska, J. Strzelecki, W. Nowak "Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods" J. Mol. Model.20 (2014), 2144-2153 DOI: DOI: 10.1007/s00894-014-2144-5
Marek Jankowski, Katarzyna Wertheim-Tysarowska, R. Jakubowski, Justyna Sota, W. Nowak, Rafal Czajkowski "Novel KRT14 mutation causing epidermolysis bullosa simplex with variable phenotype" EXP DERMATOL23 (2014), 684-687 DOI: 10.1111/exd.12478
R. Jakubowski, Piotr Skrzyniarz, Ł. Pepłowski, W. Nowak "Transthyretin Induced Amyloidosis Interactions, Mechanisms and Potent Drugs Design" Biophys. J. Suppl. 106 (2014), 661a DOI: 10.1016/j.bpj.2013.11.3659
2013
M. Dąbrowski, W. Nowak, prof. dr hab. Stankiewicz Maria "An influence of neuroactive compounds on insect ion channels" Eur. Biophys. J. Biophys. Lett. Suppl.42 (2013), 79-79 DOI: 10.1007/s00249-013-0917-x
Ł. Pepłowski, Joanna Estkowska, W. Nowak "Electric field effects on EGF and bFGF ligand- receptor unbinding investigated by Steered MD method" Eur. Biophys. J. Biophys. Lett. Suppl.42 (Suppl 1) (2013), S94-S94 DOI: 10.1007/s00249-013-0917-x
P. Miszta, S. C. Basak, R. Natarjan, W. Nowak "How Computational Studies of Mosquito Repellents Contribute to the Control of Vector Born Diseases" Current Computer-Aided Drug Design9(3) (2013), 300-307 DOI: 10.2174/15734099113099990018
Anna Gogolińska, W. Nowak "Molecular basis of lateral force spectroscopy nano-diagnostics: computational unbinding of autism related chemokine MCP-1 from IgG antibody" J. Mol. Model.Volume 19, Issue 11 (2013), 4773-4780 DOI: 10.1007/s00894-013-1972-z
K. Mikulska-Rumińska, W. Nowak "Nanomechanics of proteins related to autism spectrum disorder" Eur. Biophys. J. Biophys. Lett. Suppl.42 (Suppl 1) (2013), S94 DOI: DOI 10.1007/s00249-013-0917-x
K. Mikulska-Rumińska, R. Jakubowski, Ł. Pepłowski, M. Dąbrowski, A. Gogolińska, Włodzisław Duch, W. Nowak "On applications of virtual atomic force microscope in studies of brain proteins" Eur. Biophys. J. Biophys. Lett. Suppl. 42 (Suppl 1) (2013), S93-S93 DOI: DOI 10.1007/s00249-013-0917-x
D. Bielińska-Wąż, dr Wąż Piotr, prof. Clark Timothy, dr hab. Puzyn Tomasz, Ł. Pepłowski, W. Nowak "Statistical properties of spectra of chloronaphthalenes" J. Math. Chem.51 (2013), 857-867 DOI: 10.1007/s10910-012-01117-4
2012
J. Strzelecki, M. Dąbrowski, dr Strzelecka Joanna, dr Tszydel Mariusz, K. Mikulska-Rumińska, W. Nowak, A. Balter "AFM Investigation of Biological Nanostructures" Acta Phys. Pol. A122 (2012), 329-332
A. Jasiński, K. Mikulska-Rumińska, B. Krajnik, S. Maćkowski, W. Nowak "Dynamics of Protein Elements of Hybrid Nanostructures - Molecular Dynamics Simulations of Light Harvesting Peridinin-Chlorophyll a-Protein Model " Acta Phys. Pol. A122 (2012), 284-288
M. Dąbrowski, W. Nowak, Jankowska Milena, prof. dr hab. Stankiewicz Maria "How experimental conditions can influence the effects of toxins binding to "site 3" on sodium channel - electrophysiological observations" Acta Neurobiol. Exp.72 (2012), 199-199
K. Mikulska-Rumińska, J. Strzelecki, A. Balter, W. Nowak "Nanomechanical unfolding of α-neurexin - a major component of the synaptic junction" Chem. Phys. Lett.521 (2012), 134-137 DOI: 10.1016/j.cplett.2011.11.033
2011
Ł. Pepłowski, Sikora Mateusz, W. Nowak, Cieplak Marek " Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations " J. Chem. Phys.134 (2011), 085102-085116 DOI: doi:10.1063/1.3553801
Ł. Pepłowski, R. Jakubowski, W. Nowak "Molecular dynamics study of bNeurexin-Neuroligin interactions" Eur. Biophys. J. Biophys. LettVolume 40, Supplement 1 (2011), S114-S114 DOI: 10.1007/s00249-011-0734-z
Anna Gogolińska, W. Nowak "Molecular recognition at atomic level: interaction of autism related protein MCP-1 with an antibody" Eur. Biophys. J. Biophys. Lett40 (2011), S106-S106 DOI: 10.1007/s00249-011-0734-z
K. Mikulska-Rumińska, Ł. Pepłowski, W. Nowak "Nanomechanics of Ig-like domains of human contactin (BIG-2)" J. Mol. Model.17 (2011), 2313-2323 DOI: 10.1007/s00894-011-1010-y
K. Mikulska-Rumińska, J. Strzelecki, A. Balter, W. Nowak "Nanomechanics of neuronal junction – stretching FNIII domains of human contactins" Eur. Biophys. J. Biophys. Lett40 (2011), S220-S220 DOI: 10.1007/s00249-011-0729-9
J. Strzelecki, J. Strzelecka, K. Mikulska-Rumińska, M.Tszydel, A. Balter, W. Nowak "Nanomechanics of new materials - AFM and computer modelling studies of trichoptera silk" Cent. Eur. J. Phys.9 (2) (2011), 482-491
2009
J. Strzelecki, K. Mikulska-Rumińska, Małgorzata Lekka, Andrzej Kulik, A. Balter, W. Nowak "AFM force spectroscopy and steered molecular dynamics simulation of protein Contactin 4" Acta Phys. Pol. A Suppl.116 (2009), 156-159
W. Nowak "Intracellular nanomanipulation by a photonic-force microscope with real-time acquisition of a 3D stiffness matrix" Nanotechnology20 (2009), 285709-285718
J. Strzelecki, K. Mikulska-Rumińska, A. Balter, W. Nowak "Single molecule AFM force spectroscopy and steered molecular dynamics of Contactin-4 protein" Eur. Biophys. J. Biophys. Lett. Suppl.38 (Suppl 1) (2009), S117-S117
2008
Ł. Pepłowski, K. Kubiak-Ossowska, S. Zelek, W. Nowak "A Comparative DFT Study of Substrates and Products of Industrial Enzyme Nitrile Hydratase" Int. J. Quantum Chem.108 (2008), 161-179
Ł. Pepłowski, K. Kubiak-Ossowska, W. Nowak "Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095" Chem. Phys. Lett.467 (2008), 144-149
K. Kubiak-Ossowska, W. Nowak "Molecular Dynamics Simulations of The Photoactive Protein Nitrile Hydratase" Biophys. J.94 (2008), 3824-3838
D. Bielińska-Wąż, W. Nowak, Ł. Pepłowski, P. Wąż, S.C. Basak, R. Natarajan "Statistical spectroscopy as a tool for the study of molecular similarity" J. Math. Chem.43 (2008), 1560-1572
D. Bielińska-Wąż, T.Clark, P. Wąż, W. Nowak, A.Nandy "2D-dynamic representation of DNA sequences" Chem. Phys. Lett.442 (2007), 140-144
D. Bielińska-Wąż, W. Nowak, P.Wąż, A.Nandy, T.Clark "Distribution moments of 2D-graphs as descriptors of DNA sequences" Chem. Phys. Lett.443 (2007), 408-413
Ł. Pepłowski, K. Kubiak-Ossowska, W. Nowak "Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides" J. Mol. Model.13 (2007), 725-730
W. Nowak "Introduction to Stochastic Search and Optimization. Estimation, Simulation, and Control" IEEE Trans/ Neural Net.18 (2007), 964-965
S. Orłowski, W. Nowak "Locally enhanced sampling molecular dynamics study of the dioxygen transport in human Cytoglobin" J. Mol. Model.13 (2007), 715-723
S. Orłowski, W. Nowak "Oxygen Diffusion in Minihemoglobin from cerebratus lacteus - a Locally Enhanced Sampling Study" Theor. Chem. Acc.117 (2007), 253-258
S.C. Basak, R. Natarajan, W. Nowak, P. Miszta, J. Klun "Three dimensional structure-activity relationships (3D-QSAR) for insect repellency of diastereomeric compounds: A hierarchical molecular overlay approach" SAR QSAR Environ Res.18 (2007), 237-250 DOI: 10.1080/10629360701303784
2004
Z.Lu, W. Nowak, G.Lee, P.Marszalek, W.Yang "Elastic properties of single amylose chains in water: a quantum mechanical and AFM study" J. Am. Chem. Soc.126 (2004), 9033-9041
G.Lee, W. Nowak, J.Jaroniec, Q.Zhang, P.E.Marszalek "Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides" Biophys. J.87 (2004), 1456-1465
G.Lee, W. Nowak, J.Jaroniec, Q.Zhang, P.E.Marszalek "Nanomechanical Control of Glucopyranose Rotamers" J. Am. Chem. Soc.126 (2004), 6218-6219
2003
K. Kubiak-Ossowska, Malgorzata Kowalska, W. Nowak "Molecular dynamics Study of Early Events During Photooxidation of Eye Lens Protein γB-crystallin" J. Mol. Struct.630 (2003), 315 -325
2002
W. Nowak "Density Functional Study on Geometry and Electronic Structure of Nitrile Hydratase Active Site Model" Int. J. Quantum Chem.90 (2002), 1174-1187
2001
W. Nowak, V.Cody, A.Wojtczak "Computer modeling studies of the structural role of NADPH binding to active site mutants of human dihydrofolate reductase in complex with piretrexim" Acta Biochim. Pol.48 (2001), 903-916
1999
Szubiakowski Jacek, A. Balter, W. Nowak, Wiśniewski Krzysztof, Aleksandrzak Krzysztof "Substituent-sensitive anisotropic rotations of 9-acetoxy-10-phenylanthracenes. Fluorescence anisotropy decay and quantum-mechanical study " Chem. Phys. Lett.313 (1999), 473-483