BIOmodeling

Publications since 2001

updated: January 2024

2021-2024

M. Krajewska, M. Możajew, S. Filipek, P. Koprowski	Interaction of ROMK2 channel with lipid kinases DGKE and AGK: potential channel activation by localized anionic lipid synthesis	BBA - Molecular and Cell Biology of Lipids (2024) 1869, 159443.	DOI
K. Szot-Karpińska, P. Kudła, U. Orzeł, M. Narajczyk, M. Jönsson-Niedziółka, B. Palys, S. Filipek, A. Ebner, J. Niedziółka-Jönsson	Investigation of peptides for molecular recognition of C-reactive protein – theoretical and experimental studies	Analytical Chemistry (2023) 95, 14475-14483.	DOI
U. Orzeł, P. Pasznik, P. Miszta, M. Lorkowski, S. Niewieczerzał, J. Jakowiecki, S. Filipek	GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex	Nucleic Acids Res. (2023) 51, W251-W262.	DOI
J. Jakowiecki, U. Orzeł, A. Gliździnska, M. Możajew, S. Filipek	chapter "Specificities of Protein Homology Modeling for Allosteric Drug Design" in book "Homology Modeling"	(Methods in Molecular Biology series, vol. 2627), Ed. S. Filipek (2023) pp. 339-348.	DOI
N. Gniado, A. Krawczyk-Balska, P. Mehta, P. Miszta, S. Filipek	"Protein Homology Modeling for Effective Drug Design" in book "Homology Modeling"	(Methods in Molecular Biology series, vol. 2627), Ed. S. Filipek (2023) pp. 329-337.	DOI
P. Miszta, P. Pasznik, S. Niewieczerzał, K. Młynarczyk, S. Filipek	COGRIMEN: Coarse-Grained Method for Modeling of Membrane Proteins in Implicit Environments	Journal of Chemical Theory and Computation 2022 18 (9), 5145-5156.	DOI
J. Żuk, D. Bartuzi, P. Miszta, A.A. Kaczor	The Role of Lipids in Allosteric Modulation of Dopamine D2 Receptor—In Silico Study	Molecules (2022) 27, 1335.	DOI
M. Berdyński, P. Miszta, K. Safranow, P.M. Andersen, M. Morita, S. Filipek, C. Żekanowski, M. Kuźma-Kozakiewicz	SOD1 mutations associated with amyotrophic lateral sclerosis analysis of variant severity	Scientific Reports (2022) 12, 103.	DOI
P. Miszta, E. Nazaruk, D. Nieciecka, M. Możajew, P. Krysiński, R. Bilewicz, S. Filipek	The EcCLC antiporter embedded in the lipidic liquid crystalline films – molecular dynamics simulations and electrochemistry	Phys. Chem. Chem. Phys. (2022) 24, 3066-3077.	DOI
O. Michalak, P. Cmoch, A. Leś, M. Cybulski, P. Krzeczyński, K. Trzcińska, P. Miszta, P. Mehta, S. Filipek	Unexpected Reaction Products of Uracil and Its Methyl Derivatives with Acetic Anhydride and Methylene Chloride	J. Org. Chem. (2021) 86, 14321-14332.	DOI
B.S. Choudhary, Sukanya, P. Mehta, S. Bach, S. Ruchaud, T. Robert, B. Josselin, S. Filipek, R. Malik	Discovery of thiazolidin-4-one analogue as selective GSK-3β inhibitor through structure based virtual screening	Bioorg. Med. Chem. Lett. (2021) 52, 128375.	DOI
U. Orzeł, J. Jakowiecki, K. Młynarczyk, S. Filipek	The role of cholesterol in amyloidogenic substrate binding to the γ secretase complex	Biomolecules (2021) 11, 935.	DOI
P. Miszta, P. Pasznik, S. Niewieczerzał, J. Jakowiecki, S. Filipek	GPCRsignal: webserver for analysis of the interface between G-protein–coupled receptors and their effector proteins by dynamics and mutations	Nucleic Acids Res. (2021) 49, W247-W256.	DOI
J. Jakowiecki, R. Abel, U. Orzeł, P. Pasznik, R. Preissner, S. Filipek	Allosteric Modulation of the CB1 Cannabinoid Receptor by Cannabidiol - A Molecular Modeling Study of the N-Terminal Domain and the Allosteric-Orthosteric Coupling	Molecules (2021) 26, 2456.	DOI
P. Mehta, P. Miszta, S. Filipek	Molecular Modeling of Histamine Receptors – Recent Advances in Drug Discovery	Molecules (2021) 26, 1778.	DOI
P. Miszta, S. Niewieczerzał, P. Pasznik, S. Filipek	chapter "Homology modeling using GPCRM web service" in book "G Protein-Coupled Receptor Screening Assays. Methods and Protocols" (Methods in Molecular Biology series), 2nd Edition	Eds S.A.M. Martins, D.M.F. Prazeres, Springer (2021) pp. 305-321.	DOI

2016-2020

P. Mehta, P. Miszta, P. Rzodkiewicz, O. Michalak, P. Krzeczyński, S. Filipek	Enigmatic histamine receptor H4 for potential treatment of multiple inflammatory, autoimmune and related diseases	Life (2020) 10, 50.	DOI
J. Jakowiecki, U. Orzeł, S. Chawananon, P. Miszta, S. Filipek	The hydrophobic ligands entry and exit from the GPCR binding site - SMD and SuMD simulations	Molecules (2020), 25, 1930.	DOI
I. Rodríguez-Espigares, M. Torrens-Fontanals, J.K.S. Tiemann, D. Aranda-García, J.M. Ramírez-Anguita, T.M. Stepniewski, N. Worp, A. Varela-Rial, A. Morales-Pastor, B.M. Lacruz, G. Pándy-Szekeres, E. Mayol, R. Fonseca, T. Giorgino, J. Carlsson, X. Deupi, S. Filipek, J.C. Gómez-Tamayo, A. Gonzalez, H. Gutierrez-de-Teran, M. Jimenez, W. Jespers, J. Kapla, P. Kolb, D. Latek, M. Marti-Solano, P. Matricon, M.T. Matsoukas, P. Miszta, M. Olivella, L. Perez-Benito, S. Ríos, I. Rodríguez-Torrecillas, J. Sallander, A. Sztyler, S. Vasile, P.W. Hildebrand, G. De Fabritiis, D.E. Gloriam, A. Cordomi, R. Guixà-González, J. Selent	GPCRmd uncovers the dynamics of the 3D-GPCRome	Nature Methods (2020) 17, 777-787.	DOI
J. Jakowiecki, P. Miszta, S. Niewieczerzał, S. Filipek	chapter „Structural Diversity in Ligand Recognition by GPCRs”, in book “GPCRs: Structure, Function, and Drug Discovery”, B. Jastrzebska and P.S.H. Park (Eds)	Elsevier Academic Press 2020, pp. 43-63.	DOI
D.Y. Zhao, M. Poege, T. Morizumi, S. Gulati, N. van Eps, J. Zhang, P. Miszta, S. Filipek, J. Mahamid, J.M. Plitzko, W. Baumeister, O.P. Ernst, K. Palczewski	Cryo-EM structure of the native rhodopsin dimer in nanodiscs	J. Biol. Chem. (2019) 294, 14215-14230.	DOI
S. Senapati, A. Poma, M. Cieplak, S. Filipek, P. Park	"Differentiating between inactive and active states of rhodopsin by atomic force microscopy in native membranes"	Anal. Chem. (2019) 91:7226-7235.	DOI
S. Yuan, T. Dahoun, M. Brugarolas, H. Pick, S. Filipek, H. Vogel	Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds	Commun. Biol. (Nature) (2019) 2:141.	DOI
S. Filipek	"Molecular switches in GPCRs"	Curr. Op. Str. Biol. (2019) 55:114–120.	DOI
D. Latek, B. Trzaskowski, S. Niewieczerzał, P. Miszta, K. Młynarczyk, A. Debinski, W. Pulawski, S. Yuan, A. Sztyler, U. Orzel, J. Jakowiecki, S. Filipek	chapter "Modeling of Membrane Proteins" in "Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes", A. Liwo (Ed.)	Springer series in Bio- and Neurosystems, Springer Nature Switzerland AG, vol. 8, ed. 2, 2019, pp. 371–451.	DOI
D. Latek, B. Trzaskowski, S. Niewieczerzał, P. Miszta, K. Młynarczyk, A. Dębiński, W. Puławski, S. Yuan, A. Sztyler, U. Orzeł, J. Jakowiecki, S. Filipek	chapter Modeling of Membrane Proteins, in Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, A. Liwo (Ed.)	Springer series in Bio- and Neurosystems, Springer-Verlag, Berlin Heidelberg, vol. 8, ed. 2, 2019, pp. 371–451	DOI
D. Latek, E. Rutkowska, S. Niewieczerzał, J. Cielecka-Piontek	Drug-induced diabetes type 2: in silico study involving class B GPCRs.	PLOS ONE (2019) 14, e0208892	DOI
P. Pasznik, E. Rutkowska, S. Niewieczerzał, J. Cielecka-Piontek, D. Latek	Potential off-target effects of beta-blockers on gut hormone receptors: in silico study including GUT-DOCK - a web service for small-molecule docking.	PLOS ONE (2019) 14, e0210705	DOI
S. Filipek	Molecular switches in GPCRs	Curr. Op. Str. Biol. (2019) 55:114–120	DOI
S. Yuan, T. Dahoun, M. Brugarolas, H. Pick, S. Filipek, H. Vogel	Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds	Commun. Biol. (Nature) (2019) 2:141	DOI
S. Senapati, A. Poma, M. Cieplak, S. Filipek, P. Park	Differentiating between inactive and active states of rhodopsin by atomic force microscopy in native membranes	Anal. Chem. (2019) 91:7226-7235	DOI
K. Synoradzki, P. Miszta, E. Kazlauskas, A. Mickeviciute, V. Michailoviene, D. Matulis, S. Filipek, P. Bieganowski	Interaction of the middle domains stabilizes Hsp90α dimer in a closed conformation with high affinity for p23	Biol. Chem. (2018) 399, 337-345	DOI
H.C.S Chan, J. Wang, K. Palczewski, S. Filipek, H. Vogel, Z.J. Liu, S. Yuan	Exploring a new ligand binding site of G protein-coupled receptors	Chem. Sci. (2018) 9, 6480–6489	DOI
P. Miszta, P. Pasznik, J. Jakowiecki, A. Sztyler, D. Latek, S. Filipek	GPCRM - a homology modeling web service with triple membrane-fitted quality assessment of GPCR models	Nucleic Acids Res. (2018) 46, W387-W395. Web Server Issue (W1)	DOI
J. Jakowiecki, A. Sztyler, S. Filipek, P. Li, K. Raman, N. Barathiraja, S. Ramakrishna, J.R. Eswara, A. Altaee, A.O. Sharif, P.M. Ajayan, V. Renugopalakrishnan	Aquaporin graphene interface: relevance to point-of-care device for renal cell carcinoma and desalination	J. R. Soc. Interface Focus (2018) 8, 20170066	DOI
P. Miszta, J. Jakowiecki, E. Rutkowska, M. Turant, D. Latek, S. Filipek	chapter 12 „Approaches for Differentiation and Interconverting GPCR Agonists and Antagonists” in book “Computational Methods for GPCR Drug Discovery”	A. Heifetz (Ed.), Methods in Molecular Biology series, vol. 1705, Springer 2018, pp. 265-296	DOI
E. Rutkowska, P. Miszta, K. Mlynarczyk, J. Jakowiecki, P. Pasznik, S. Filipek, D. Latek	Application of a membrane protein structure prediction web service GPCRM to a gastric inhibitory polypeptide receptor model", in "Bioinformatics and Biomedical Engineering. IWBBIO 2017. Lecture Notes in Computer Science	I. Rojas, F. Ortuno (Eds.), vol. 10209, Springer 2017, pp. 151-162	DOI
D. Latek, B. Trzaskowski, S. Niewieczerzał, P. Miszta, K. Młynarczyk, A. Debinski, W. Pulawski, S. Yuan, S. Filipek	chapter 12 "Modeling of Membrane Proteins" in "Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes"	A. Liwo (Ed.), series in Bio-/Neuroinformatics, Springer-Verlag, Berlin Heidelberg, vol. 1, 2014, pp. 357–431	DOI
K. Synoradzki, P. Miszta, E. Kazlauskas, A. Mickeviciute, V. Michailoviene, D. Matulis, S. Filipek, P. Bieganowski	Interaction of the middle domains stabilizes Hsp90α dimer in a closed conformation with high affinity for p23	Biol. Chem. (2018) 399, 337-345	DOI
A. Jarmula, P. Wilk, P. Maj, J. Ludwiczak, A. Dowiercial, K. Banaszak, W. Rypniewski, J. Ciesla, M. Dabrowska, T. Fraczyk, A.K. Bronowska, J. Jakowiecki, S. Filipek, W. Rode	Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS	J. Mol. Graph. Model. (2017) 77, 33-50	DOI
B. Żyżyńska-Granica, B. Trzaskowski, S. Niewieczerzał, S. Filipek, O. Zegrocka-Stendel, M. Dutkiewicz, P. Krzeczyński, M. Kowalewska, K. Koziak	Pharmacophore guided discovery of small-molecule interleukin 15 inhibitors	Eur. J. Med. Chem. (2017) 136, 543-547	DOI
S. Gulati, B. Jastrzebska, S. Banerjee, A. Placeres, P. Miszta, S. Gao, K. Gunderson, G. Tochtrop, S. Filipek, K. Katayama, P.D. Kiser, M. Mogi, P.L. Stewart, K. Palczewski	Photocyclic behavior of rhodopsin induced by a novel isomerization mechanism	Proc. Natl. Acad. Sci. USA (2017) 114, E2608-E2615.	DOI
M. Bajda, S. Filipek	Computational approach for the assessment of inhibitory potency against beta-amyloid aggregation	Bioorg. Med. Chem. Lett. (2017) 27, 212-216.	DOI
J.P. Fichna, A. Potulska-Chromik, P. Miszta, M.J. Redowicz, A.M. Kaminska, C. Zekanowski, S. Filipek	A novel dominant D109A CRYAB mutation in a family with myofibrillar myopathy affects αB-crystallin structure	BBA Clin. (2017) 7, 1-7.	DOI
J. Jakowiecki, S. Filipek	Hydrophobic ligands entry and exit pathways of CB1 cannabinoid receptor	J. Chem. Inf. Model. (2016) 56, 2457-2466.	DOI
S. Yuan, H.C.S. Chan, S. Filipek, H. Vogel	PyMOL and Inkscape bridge the data and the data visualization	Structure (2016) 24, 2041–2042.	DOI
H.C.S. Chan, S. Filipek, S. Yuan	The principles of ligand specificity on beta-2-adrenergic receptor	Sci. Rep. Nature (2016) 6, 34736.	DOI
E. Simoni, R. Caporaso, C. Bergamini, J. Fiori, R. Fato, P. Miszta, S. Filipek, F. Caraci, M.L. Giuffrida, V. Andrisano, A. Minarini, M. Bartolini, M. Rosini	Polyamine conjugation as a promising strategy to target amyloid aggregation in the framework of Alzheimer’s disease	ACS Med. Chem. Lett. (2016) 7, 1145-1150.	DOI
A.K. Mishra, M. Gragg, M. Stoneman, G. Biener, J.A. Oliver, P. Miszta, S. Filipek, V. Raicu, P.S.H. Park	Quaternary structures of opsin in live cells revealed by FRET spectrometry	Biochem. J. (2016) 473, 3819-3836.	DOI
T. Lazarova, K. Mlynarczyk, E. Querol, B. Tenchov, S. Filipek, E. Padros	Identification of Specific Effect of Chloride on the Spectral Properties and Structural Stability of Multiple Extracellular Glutamic Acid Mutants of Bacteriorhodopsin	PLOS ONE (2016) 11, e0162952.	DOI
S. Yuan, H.C.S. Chan, H. Vogel, S. Filipek, R.C. Stevens, K. Palczewski	The molecular mechanism of P2Y1 receptor activation	Angew. Chem. Int. Ed. (2016) 55, 10331-10335.	DOI
S. Yuan, Q. Peng, K. Palczewski, H. Vogel, S. Filipek	Mechanistic studies on the stereoselectivity of the serotonin 5-HT1A receptor	Angew. Chem. Int. Ed. (2016) 55, 8661-8665.	DOI
S. Montanari, M. Bartolini, P. Neviani, F. Belluti, S. Gobbi, L. Pruccoli, A. Tarozzi, F. Falchi, V. Andrisano, P. Miszta, S. Filipek, A. Cavalli, A. Bisi, A. Rampa	Multi-target strategy to address Alzheimer’s disease: design, synthesis, biological evaluation and computational studies of coumarin-based derivatives	ChemMedChem (2016) 11, 1296-1308.	DOI
S. Yuan, S. Filipek, H. Vogel	A gating mechanism of the serotonin 5-HT3 receptor	Structure (2016) 24, 816-825.	DOI
D. Latek, M. Bajda, S. Filipek	A hybrid approach to structure and function modeling of G protein-coupled receptors	J. Chem. Inf. Model. (2016) 56, 630-641.	DOI

2011-2015

E. Nazaruk, P. Miszta, S. Filipek, E. Gorecka, E. Landau, R. Bilewicz	Lyotropic Cubic Phases for Drug Delivery: Diffusion and Sustained Release from the Mesophase Evaluated by Electrochemical Methods	Langmuir (2015) 31, 12753-12761.	DOI
S. Viswanathan, T.N. Narayanan, K. Aran, K.D. Fink, J. Paredes, P.M. Ajayan, S. Filipek, P. Miszta, H.C. Tekin, F. Inci, U. Demirci, P. Li, K.I. Bolotin, D. Liepmann, V. Renugopalakrishnan	Graphene–protein field effect biosensors: glucose sensing	Mater. Today (2015) 18, 513-522.	DOI
A. Hernik, W. Pulawski, B. Fedorczyk, D. Tymecka, A. Misicka, S. Filipek, W. Dzwolak	Amyloidogenic properties of short α-L-glutamic acid oligomers	Langmuir (2015) 31, 10500-10507.	DOI
O. Baud, S. Yuan, L. Veya, S. Filipek, H. Vogel, H. Pick	Exchanging ligand-binding specificity between a pair of mouse olfactory receptor paralogs reveals odorant recognition principles	Sci. Rep. Nxature (2015) 5, 14948.	DOI
T.M. Stepniewski, S. Filipek	Non-peptide ligand binding to the formyl peptide receptor FPR2 - a comparison to peptide ligand binding modes	Bioorg. Med. Chem. (2015) 23, 4072-4081.	DOI
M. Bajda, S. Filipek	Study of early stages of amyloid A 13-23 formation using molecular dynamics simulation in implicit environments	Comput. Biol. Chem. (2015) 56, 13-18.	DOI
S. Yuan, K. Palczewski, Q. Peng, M. Kolinski, H. Vogel, S. Filipek	The mechanism of ligand-induced activation or inhibition of mu- and kappa-opioid receptors	Angew. Chem. Int. Ed. (2015) 54, 7560-7563.	DOI
S. Yuan, Z. Hu, S. Filipek, H. Vogel	W246[6.48] opens a gate for a continuous intrinsic water pathway during activation of the adenosine A2A receptor.	Angew. Chem. Int. Ed. (2015) 54, 556-559.	DOI
U. Ghoshdastider, R. Wu, B. Trzaskowski, K. Mlynarczyk, P. Miszta, M. Gurusaran, S. Viswanathan, V. Renugopalakrishnan, S. Filipek	Molecular Effects of Encapsulation of Glucose Oxidase Dimer by Graphene.	RSC Advances (2015) 5, 13570-13578.	DOI
J.P. Fichna, J. Karolczak, A. Potulska-Chromik, P. Miszta, M. Berdynski, A. Sikorska, S. Filipek, M.J. Redowicz, A. Kaminska, C. Zekanowski	Two desmin gene mutations associated with myofibrillar myopathies in Polish families.	PLOS ONE (2014) 9, e115470.	DOI
I. Kufareva, V. Katritch, Participants of GPCR DOCK 2013, R.C. Stevens, R. Abagyan	Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges.	Structure (2014) 22, 1120-1139.	DOI
S. Yuan, S. Filipek, K. Palczewski, H. Vogel	Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway.	Nat. Commun. (2014), 5, 4733.	DOI
T. Lazarova, K. Mlynarczyk, S. Filipek, M. Kolinski, T.J. Wassenaar, M.E. Querol, V. Renugopalakrishnan, S. Viswanathan, E. Padrós	The Effect of Triple Glutamic Mutations E9Q/E194Q/E204Q on the Structural Stability of Bacteriorhodopsin	FEBS J. (2014) 281, 1181-1195.	DOI
M. Bajda, J. Jonczyk, B. Malawska, S. Filipek	Application of computational methods for the design of BACE-1 inhibitors: validation of in silico modelling	Int. J. Mol. Sci. (2014) 15, 5128-5139.	DOI
S.A. Shahzad, M. Yar, M. Bajda, B. Jadoon, Z.A. Khan, S.A. Naqvi, A.J. Shaikh, K. Hayat, A. Mahmmod, N. Mahmood, S. Filipek	Synthesis and biological evaluation of novel oxadiazole derivatives: A new class of thymidine phosphorylase inhibitors as potential anti-tumor agents	Bioorg. Med. Chem. (2014) 22, 1008-1015.	DOI
D. Latek, B. Trzaskowski, S. Niewieczerzał, P. Miszta, K. Młynarczyk, A. Debinski, W. Pulawski, S. Yuan, S. Filipek	chapter Modeling of Membrane Proteins in Computational methods to study the structure and dynamics of biomolecules and biomolecular processes – from bioinformatics to molecular quantum mechanics	ed. A. Liwo, Springer Series in Bio-/Neuroinformatics, vol. 1, 2014, pp. 357–431.	DOI
C. Roos, L. Kai, S. Haberstock, D. Proverbio, U. Ghoshdastider, Y. Ma, S. Filipek, X. Wang, V. Dötsch, F. Bernhard	chapter 7 High Level Cell-Free Production of Membrane Proteins with Nanodiscs in Cell-Free Protein Synthesis	A. Kirill, W.A. Johnston, (Eds.), series „Methods in Molecular Biology”, Humana Press, vol. vol. 1118, 2014, pp. 109-130.	DOI
S. Yuan, H. Vogel, S. Filipek	The Role of Water and Sodium Ions in the Activation of the mu-Opioid Receptor	Angew. Chem. Int. Ed. (2013) 52, 10112-10115.	DOI
E.J. Sitek, E. Narozanska, B. Peplonska, S. Filipek, A. Barczak, M. Styczynska, K. Mlynarczyk, B. Brockhuis, E. Portelius, D. Religa, M. Barcikowska, J. Slawek, C. Zekanowski	A patient with posterior cortical atrophy possesses a novel mutation in the presenilin 1 gene	PLOS ONE (2013) 8, e61074.	DOI
S. Yuan, R. Wu, D. Latek, B. Trzaskowski, S. Filipek	Lipid receptor S1P1 activation scheme concluded from microsecond all-atom molecular dynamics simulations	PLOS Comp. Biol. (2013) 9, e1003261.	DOI
R. Nahomi, R. Huang, S. Nandi, B. Wang, S. Padmanabha, P. Santhoshkumar, S. Filipek, A. Biswas, R. Nagaraj	Acetylation of Lysine92 Improves the Chaperone and Anti-apoptotic Activities of Human αB-Crystallin	Biochemistry (2013) 52, 8126–8138.	DOI
L. Skjaerven, L. Codutti, A. Angelini, M. Grimaldi, D. Latek, P. Monecke, M. Dreyer, T. Carlomagno	Accounting for Conformational Variability in Protein-Ligand Docking with NMR-Guided Rescoring	J. Am. Chem. Soc. (2013) 135, 5819-5827.	DOI
D. Latek, P. Pasznik, T. Carlomagno, S. Filipek	Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison	PLOS ONE (2013) 8(2): e56742	DOI
P. Miszta, S.C. Basak, R. Natarajan, W. Nowak	How computational studies of mosquito repellents contribute to the control of vector Borne Diseases	Curr. Comput. Aided Drug Des. (2013) 9, 300-307.	DOI
W. Pulawski, S. Filipek, A. Zwolinska, A. Debinski, K. Krzysko, R. Garduno-Juarez, S. Viswanathan, V. Renugopalakrishnan	Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data	Eur. Biophys. J. (2013) 42, 291-300.	DOI
C. Roos, L. Kai, D. Proverbio, U. Ghoshdastider, S. Filipek, V. Dötsch, F. Bernhard	Co-translational association of cell-free expressed membrane proteins with supplied lipid bilayers	Mol. Membr. Biol. (2013) 30, 75-89.	DOI
D. Latek, A. Modzelewska, B. Trzaskowski, K. Palczewski, S. Filipek	G Protein-Coupled Receptors - Recent Advances	Acta Biochim. Pol. (2012) 59, 515-529.	DOI
S. Yuan, U. Ghoshdastider, B. Trzaskowski, D. Latek, A. Debinski, W. Pulawski, R. Wu, V. Gerke, S. Filipek	The role of water in activation mechanism of human N-formyl Peptide Receptor 1 (FPR1) based on molecular dynamics simulations	PLOS ONE (2012) 7, e47114.	DOI
M. Naldi, J. Fiori, M. Pistolozzi, A.F. Drake, C. Bertucci, R. Wu, K. Mlynarczyk, S. Filipek, A. De Simone, V. Andrisano	Amyloid beta-peptide 25-35 self-assembly and its inhibition: a model undecapeptide system to gain atomistic and secondary structure details of the Alzheimer’s disease process and treatment	ACS Chem. Neurosci. (2012) 3, 952-62.	DOI
S. Dreisigacker, D. Latek, S. Bockelmann, M. Huss, H. Wieczorek, S. Filipek, H. Gohlke, D. Menche, T. Carlomagno	Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase	J. Chem. Inf. Model. (2012) 52, 2265–2272.	DOI
P. Shaik Syed Ali, U. Ghoshdastider, J. Hoffmann, B. Brutschy, S. Filipek	Recognition of the let-7g miRNA precursor by human Lin28B	FEBS Lett. (2012) 586: 3986-3990.	DOI
Y. Ma, U. Ghoshdastider, J. Wang, W. Ye, V. Dötsch, S. Filipek, F. Bernhard, X. Wang	Fast and efficient synthesis of functional GNA1 using cell-free expression	Protein Expr Purif. (2012) 86, 120-126.	DOI
B. Trzaskowski, D. Latek, S. Yuan, U. Ghoshdastider, A. Debinski, S. Filipek	Action of molecular switches in GPCRs - theoretical and experimental studies	Curr. Med. Chem. (2012) 19, 1090-1109.	DOI
W. Pulawski, U. Ghoshdastider, V. Andrisano, S. Filipek	Ubiquitous Amyloids	Appl. Biochem. Biotech. (2012) 166, 1626-1643.	DOI
S. Viswanathan, P. Li, W. Choi, S. Filipek, T.A. Balasubramaniam, V. Renugopalakrishnan	chapter Protein-Carbon Nanotube Sensors: Single Platform Integrated Micro Clinical Lab for Monitoring Blood Analytes	Method. Enzymol. (2012) 509, 165-194.	DOI
N. Santhanamoorthi, P. Kolandaivel, L. Adler−Abramovich, E. Gazit, S. Filipek, S. Viswanathan, A. Strzelczyk, V. Renugopalakrishnan	Diphenylalanine peptide nanotube: charge transport, band gap and its relevance to potential biomedical applications	Adv. Mat. Lett. (2011) 2, 100-105.	DOI
G.F. Audette, S. Lombardo, J. Dudzik, T.M. Arruda, M. Kolinski, S. Filipek, S. Mukerjee, A.M. Kannan, V. Thavasi, S. Ramakrishna, M. Chin, P. Somasundaran, S. Viswanathan, R.S. Keles, V. Renugopalakrishnan	Protein hot spots at bio-nano interfaces	Mater. Today (2011) 14, 360-365.	DOI
B. Jastrzebska, A. Debinski, S. Filipek, K. Palczewski	Role of Membrane Integrity on G protein-coupled Receptors: Rhodopsin Stability and Function	Prog. Lipid Res. (2011) 22, 267-277.	DOI
D. Latek, M. Kolinski, U. Ghoshdastider, A. Debinski, R. Bombolewski, A. Plazinska, K. Jozwiak, S. Filipek	Modeling of ligand binding to G protein coupled receptors: cannabinoid CB1, CB2 and adrenergic β₂AR	J. Mol. Model. (2011) 17, 2353-2366.	DOI
E. Kilanczyk, S. Filipek, A. Filipek	ERK1/2 is dephosphorylated by a novel phosphatase - CacyBP/SIP	Biochem. Biophys. Res. Commun. (2011) 404:179-183.	DOI
I. Kufareva, M. Rueda, V. Katritch, GPCR Dock 2010 participants, R.C. Stevens, R. Abagyan	Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment	Structure (2011) 19, 1108-1126. Participation as a head of contributing research group.	DOI
R. Koch, A.S. Lipton, S. Filipek, V. Renugopalakrishnan	Arginine interactions with anatase TiO2 (100) surface and the perturbation of ⁴⁹Ti NMR chemical shifts – a DFT investigation: Relevance to Renu-Seeram Bio Solar Cell	J. Mol. Model. (2011) 17, 1467-1472.	DOI

2006-2010

P. Somasundaran, S. Viswanathan, M. Chin, S. Filipek, V. Renugopalakrishnan	Proteins Immobilized on Surfaces	J. Surface Sci. Technol. (2010) 26, 353-369.
S. Sobhanifar, B. Schneider, F. Löhr, D. Gottstein, T. Ikeya, K. Mlynarczyk, W. Pulawski, U. Ghoshdastider, M. Kolinski, S. Filipek, P. Güntert, F. Bernhard, V. Dötsch	Structural investigation of the C-terminal catalytic fragment of presenilin 1	Proc. Natl. Acad. Sci. USA (2010) 107:9644-9649.	DOI
A. Zurawska, J. Urbanski, J. Matuliene, J. Baraniak, M.P. Klejman, S. Filipek, D. Matulis, P. Bieganowski	Mutations that increase both Hsp90 ATPase activity in vitro and Hsp90 drug resistance in vivo	Biochim. Biophys. Acta – Mol. Cell Res. (2010) 1803:575-583.	DOI
M. Kolinski, S. Filipek	Structurally similar pair of agonist and antagonist of kappa opioid receptor studied by molecular dynamics simulations	J. Mol. Model. (2010) 16:1567-1576.	DOI
M. Kolinski, S. Filipek	Studies of the Activation Steps Concurrent to Ligand Binding in deltaOR and kappaOR Opioid Receptors Based on Molecular Dynamics Simulations	TOSBJ (2009) 3:51-63.	DOI
P. Park, K. Sapra, B. Jastrzebska, T. Maeda, A. Maeda, W. Pulawski, M. Kono, J. Lem, R. Crouch, S. Filipek, D. Muller, K. Palczewski	Modulation of molecular interactions and function by rhodopsin palmitylation	Biochemistry (2009) 48:4294-4304.	DOI
E. Kilanczyk, S. Filipek, B. Jastrzebska, A. Filipek	CacyBP/SIP binds ERK1/2 and affects transcriptional activity of Elk-1	Biochem. Biophys. Res. Commun. (2009) 380:54-59.	DOI
J. Austermann, A.R. Nazmi, A. Heil, G. Fritz, M. Kolinski, S. Filipek, V. Gerke	Generation and characterization of a novel, permanently active S100P mutant	Biochim. Biophys. Acta – Mol. Cell Res. (2009) 1793:1078-1085.	DOI
S. Filipek	Bioinformatyka strukturalna białek transbłonowych	Kosmos (2009) 58:57-66.	PDF
J.S. Jaworski, A. Kosson, S. Filipek, M. Kolinski, D. Kuck	Properties of Radical Anions of Triptindanones and Indanones: Electronic Communication and Stability of Ion Pairs Containing Lithium Cations	J. Phys. Chem. C (2009) 113:7436–7442.	DOI
A.M. Kannan, V. Renugopalakrishnan, S. Filipek, P. Li, G.F. Audette, L. Munukutla	Bio-Batteries and Bio Fuel Cells: Leveraging on Electronic Charge Transfer Proteins	J. Nanosci. Nanotechnol. (2009) 9:1665-1678.	DOI
V. Thavasi, T. Lazarova, S. Filipek, M. Kolinski, E. Querol, A. Kumar, S. Ramakrishna, E. Padros, V. Renugopalakrishnan	Study on the Feasibility of Bacteriorhodopsin as Bio-Photosensitizer in Excitonic Solar Cell: A First Report	J. Nanosci. Nanotechnol. (2009) 9:1679-1687.	DOI
V. Renugopalakrishnan, A. M. Kannan, S. Srinivasan, V. Thavasi, S. Ramakrishna, P. Li, A. Mershin, S. Filipek, A. Kumar, J. Dutta, A. Jaya, L. Munukutla, S. Velumani, and G. F. Audette	chapter Nanomaterials for Energy Conversion Applications, in Nanomaterials for Energy Storage Applications	H.S. Nalwa ed., American Scientific Publishers, Valencia, CA, USA (2009) pp. 155-178.
M. Kolinski, S. Filipek	Molecular Dynamics of mu Opioid Receptor Complexes with Agonists and Antagonists	TOSBJ (2008) 2:8-20.	DOI
R. Stephen, S. Filipek, K. Palczewski, M.C. Sousa	Ca(2+)-dependent Regulation of Phototransduction	Photochem. Photobiol. (2008) 84:903-910.	DOI
T. Majewski, S. Lee, J. Jeong, D.S. Yoon, A. Kram, M.S. Kim, T. Tuziak, J. Bondaruk, S. Lee, W.S. Park, K.S. Tang, W. Chung, L. Shen, S.S. Ahmed, D.A. Johnston, H.B. Grossman, J.H. Zhou, R.A. Harris, C. Snyder, S. Filipek, S.A. Narod, P. Watson, H.T. Lynch, A. Gazdar, K. Baggerly, J.P. Issa, W.F. Benedict, S.E. Scherer, B. Czerniak	Understanding the Development of Human Bladder Cancer By Using a Whole-Organ Genomic Mapping Strategy	Lab. Invest. (2008) 88:694-721.	DOI
K. Jozwiak, K.A. Krzysko, L. Bojarski, M. Gacia, S. Filipek	Molecular models of the interface between APH-1 and presenilin involving GxxxG motifs	ChemMedChem (2008) 3:627-634.	DOI
M.P. Golan, M. Styczynska, K. Jozwiak, J. Walecki, A. Maruszak, J. Pniewski, R. Lugiewicz, S. Filipek, M. Barcikowska, C. Zekanowski	Early-onset Alzheimer's disease with a de novo mutation in the presenilin 1 gene	Exp. Neurol. (2007) 208:264-268.	DOI
S. Lee, J. Jeong, T. Majewski, S.E. Scherer, M.S. Kim, T. Tuziak, K.S. Tang, K. Baggerly, H.B. Grossman, J.H. Zhou, L. Shen, J. Bondaruk, S.S. Ahmed, S. Samanta, P. Spiess, X. Wu, S. Filipek, D. McConkey, M. Bar-Eli, J.P. Issa, W.F. Benedict, B. Czerniak	Forerunner genes contiguous to RB1 contribute to the development of in situ neoplasia	Proc. Natl. Acad. Sci. USA (2007) 104: 13732-13737.	DOI
K.A. Krzysko, M. Kolinski, S. Filipek,	Molecular modelling of the complex of oligomeric rhodopsin and its G protein	J. Phys.: Condens. Matter (2007) 19:285204.	DOI
P.S.H. Park, K.T. Sapra, M. Kolinski, S. Filipek, K. Palczewski, D.J. Muller,	Stabilizing effect of Zn²⁺ in native bovine rhodopsin	J. Biol. Chem. (2007) 282: 11377-11385.	DOI
S. Filipek, A. Modzelewska, K.A. Krzysko	chapter Dimerization and oligomerization of rhodopsin and other G protein-coupled receptors in Molecular Materials with Specific Interactions: Modeling and Design	W.A. Sokalski ed., Springer 2007, pp. 453-467.	DOI
K. Jozwiak, C. Zekanowski, S. Filipek	Linear patterns of Alzheimer's disease mutations along alpha-helices of presenilins as a tool for PS-1 model construction	J. Neurochem. (2006) 98:1560-1572.	DOI
M. Cieplak, S. Filipek, H. Janovjak, K.A. Krzysko	Pulling single bacteriorhodopsins out of a membrane: comparison of simulation and experiment	Biochim. Biophys. Acta - Biomembranes (2006) 1758:537-544.	DOI
L. Zhu, Y. Imanishi, S. Filipek, A. Alekseev, B. Jastrzebska, W. Sun, D.A. Saperstein, K. Palczewski	Autosomal recessive retinitis pigmentosa: E150K mutation in the opsin gene	J. Biol. Chem. (2006) 281: 22289-22298.	DOI
K.T. Sapra, P.S.-H. Park, S. Filipek, A. Engel, D.J. Muller, K. Palczewski	Detecting molecular interactions that stabilize native bovine rhodopsin	J. Mol. Biol. (2006) 358:255-269.	DOI
C. Zekanowski, M.P. Golan, K.A. Krzysko, D. Religa, W. Lipczynska-Lojkowska, S. Filipek, A. Kowalska, G. Rossa, B. Peplonska, M. Styczynska, A. Maruszak, M. Wender, J. Kulczycki, M. Barcikowska, J. Kuznicki	Two novel presenilin-1 gene mutations connected with frontotemporal dementia-like phenotype: genetic and bioinformatic assessment	Exp. Neurol. (2006) 200:82-88.	DOI
A. Modzelewska, S. Filipek, K. Palczewski, P.S.-H. Park	Arrestin interaction with rhodopsin: conceptual models	Cell Biochem. Biophys. (2006) 46:1-15.	DOI
S. Filipek, A. Modzelewska	chapter Molecular Modelling of Membrane Proteins, in Structural Genomics on Membrane Proteins	K.H. Lundstrom ed., Taylor and Francis, New York (2006) pp. 331-348.
J.S. Jaworski, M. Cembor, M. Kolinski	Electrostatic model of bond dissociation energies in polyhalogen methanes	J. Phys. Org. Chem. (2006) 19:276-280.	DOI

2001-2005

S. Filipek, A. Modzelewska, K.A. Krzysko	Functional Oligomers of Rhodopsin - a G Protein-Coupled Receptor Template, in Joint Meeting on Medicinal Chemistry, Vienna (Austria) June 20-23, 2005	P. Ettmayer, G. Ecker eds., Medimond International Proceedings, Bologna, Italy, 2005, pp. 5-10.
S. Filipek	Organization of rhodopsin molecules in native membranes of rod cells - old theoretical model compared to new experimental data	J. Mol. Model. (2005) 11:385-391.	DOI
I. Sokal, W.J. Dupps, M.A. Grassi, J. Brown, Jr., L.M. Affatigato, N. Roychowdhury, L. Yang, S. Filipek, K. Palczewski, E.M. Stone, W. Baehr	A Novel GCAP1 Missense Mutation (L151F) in a Large Family with Autosomal Dominant Cone-Rod Dystrophy (adCORD)	Invest. Ophth. Vis. Sci. (2005) 46:1124-1132.	DOI
P.S.H. Park, S. Filipek, J.W. Wells, K. Palczewski	Oligomerization of G protein-coupled receptors: past, present, and future	Biochemistry (2004) 43: 15643-15656.	DOI
D. Fotiadis, Y. Liang, S. Filipek, D.A. Saperstein, A. Engel, K. Palczewski	The G protein-coupled receptor rhodopsin in the native membrane	FEBS Lett. (2004) 564:281-288.	DOI
S. Filipek, K.A. Krzysko, D. Fotiadis, Y. Liang, D.A. Saperstein, A. Engel, K. Palczewski	A concept for G protein activation by G protein-coupled receptor dimers: the transducin/ rhodopsin interface	Photochem. Photobiol. Sci. (2004) 3:628-638.	DOI
B. Jastrzebska, T. Maeda, L. Zhu, D. Fotiadis, S. Filipek, A. Engel, R.E. Stenkamp, K. Palczewski	Functional characterization of rhodopsin monomers and dimers in detergents	J. Biol. Chem. (2004) 279: 54663-54675.	DOI
L. Zhu, G.F. Jang, B. Jastrzebska, S. Filipek, S.E. Pearce-Kelling, G.D. Aguirre, R.E. Stenkamp, G.M. Acland, K. Palczewski	Naturally occurring mutation of the opsin gene (T4R) in dogs affects glycosylation and stability of the G protein-coupled receptor	J. Biol. Chem. (2004) 279: 53828-53839.	DOI
Y. Liang, D. Fotiadis, T. Maeda, A. Maeda, A. Modzelewska, S. Filipek, D.A. Saperstein, A. Engel, K. Palczewski	Rhodopsin signaling and organization in heterozygote rhodopsin knockout mice	J. Biol. Chem. (2004) 279: 48189-48196.	DOI
K. Suda, S. Filipek, K. Palczewski, A. Engel, D. Fotiadis	The supramolecular structure of the GPCR rhodopsin in solution and native disc membranes	Mol. Membr. Biol. (2004) 21:435-446.	DOI
C. Zekanowski, D. Religa, C. Graff, S. Filipek, J. Kuznicki	Genetic aspects of Alzheimer's disease	Acta Neurobiol. Exp. (2004) 64:19-31.	PDF
Y. Imanishi, L. Yang, I. Sokal, S. Filipek, K. Palczewski, W. Baehr	Diversity of Guanylate Cyclase-Activating Proteins (GCAPS) in Teleost Fish: Characterization of Three Novel GCAPs (GCAP4, GCAP5, GCAP7) from Zebrafish (Danio Rerio) and P#ac1310iction of Eight GCAPs (GCAP1-8) in Pufferfish (Fugu Rubripes)	J. Mol. Evol. (2004) 59:204-217.	DOI
D. Fotiadis, Y. Liang, S. Filipek, D.A. Saperstein, A. Engel, K. Palczewski	Is rhodopsin dimeric in native rods? Reply	Nature (2003) 426:31-31.	DOI
D. Fotiadis, Y. Liang, S. Filipek, D.A. Saperstein, A. Engel, K. Palczewski	Atomic-force microscopy: Rhodopsin dimers in native disc membranes	Nature (2003) 421:127-128.	DOI
Y. Liang, D. Fotiadis, S. Filipek, D.A. Saperstein, K. Palczewski, A. Engel	Organization of the G Protein-coupled Receptors Rhodopsin and Opsin in Native Membranes	J. Biol. Chem. (2003) 278: 21655-21662.	DOI
T. Mirzadegan, G. Benko, S. Filipek, K. Palczewski	Sequence Analyses of G-Protein-Coupled Receptors: Similarities to Rhodopsin	Biochemistry-US (2003) 42: 2759-2767.	DOI
N.M. Syed, V. Kuksa, Y. Imanishi, L. Zhu, S. Filipek, K. Palczewski, S. Kaushal	Pharmacological Chaperone-mediated in Vivo Folding and Stabilization of the P23H-opsin Mutant Associated with Autosomal Dominant Retinitis Pigmentosa	J. Biol. Chem. (2003) 278: 14442-14450.	DOI
S. Filipek, D.C. Teller, K. Palczewski, R. Stenkamp	The Crystallographic Model of Rhodopsin and Its Use in Studies of Other G Protein-Coupled Receptors	Annu. Rev. Biophys. Biomol. Struct. (2003) 32:375-397.	DOI
S. Filipek, R.E. Stenkamp, D.C. Teller, K. Palczewski	G Protein-Coupled Receptor Rhodopsin: A Prospectus	Annu. Rev. Physiol. (2003) 65:851-879.	DOI
O. Fritze, S. Filipek, V. Kuksa, K. Palczewski, K.P. Hofmann, O.P. Ernst	The Role of Conserved NPXXY(X)_5,6F Motif in The Rhodopsin Ground State and During Activation	Proc. Natl. Acad. Sci. USA (2003) 100:2290-2295.	DOI
S.A. Schadel, M. Heck, D. Maretzki, S. Filipek, D.C. Teller, K. Palczewski, K.P. Hofmann	Ligand Channeling within a G-protein-coupled Receptor: The Entry and Exit of Retinals in Native Opsin	J. Biol. Chem. (2003) 278: 24896-24903.	DOI
T. Maeda, J.P. van Hooser, C.A.G.G. Driessen, S. Filipek, J.J.M. Janssen, K. Palczewski	Evaluation of the Role of the Retinal G-Protein-Coupled Receptor (RGR) in the Vertebrate Retina in Vivo	J. Neurochem. (2003) 85:944-956.	DOI
V. Kuksa, F. Bartl, T. Maeda, G.F. Jang, E. Ritter, M. Heck, J.P. Van Hooser, Y. Liang, S. Filipek, MH. Gelb, K.P. Hofmann, K. Palczewski	Biochemical and Physiological Properties of Rhodopsin Regenerated with 11-cis-6-Ring- and 7-Ring-retinals	J. Biol. Chem. (2002) 277: 42315-42324.	DOI
R.E. Stenkamp, S. Filipek, C.A.G.G. Driessen, D.C. Teller, K. Palczewski	Crystal Structure of Rhodopsin: A Template for Cone Visual Pigments and Other G Protein-Coupled Receptors	Biochim. Biophys. Acta - Biomembranes (2002) 1565:168-182.	DOI
F. Haeseleer, Y. Imanishi, I. Sokal, S. Filipek, K. Palczewski	Calcium-Binding Proteins: Intracellular Sensors from the Calmodulin Superfamily	Biochem. Biophys. Res. Commun. (2002) 290:615-623.	DOI
G.-F. Jang, V. Kuksa, S. Filipek, F. Bartl, E. Ritter, M.H. Gelb, K.P. Hofmann, K. Palczewski	Mechanism of Rhodopsin Activation as Examined with Ring Constrained Retinal Analogs and the Crystal Structure of the Ground State Protein	J. Biol. Chem. (2001) 276(28): 26148-26153.	DOI
I. Sokal, N. Li, C.S. Klug, S. Filipek, W.L. Hubbell, W. Baehr, K. Palczewski	Calcium-sensitive Regions of GCAP1 as Observed by Chemical Modifications, Fluorescence, and EPR Spectroscopies	J. Biol. Chem. (2001) 276(46): 43361-43373.	DOI
A. Bronowska, A. Les, Z. Chilmonczyk, S. Filipek, O. Edvardsen, R. Ostensen, I. Sylte	Molecular Dynamics of Buspirone Analogues Interacting with the 5-HT_1A and 5-HT_2A Serotonin Receptors	Bioorg. Med. Chem. (2001) 9(4):881-895.	DOI
Z. Chilmonczyk, D. Siluk, R. Kaliszan, B. Lozowicka, J. Poplawski, S. Filipek	New chemical structures of hypolipidemic and antiplatelet activity	Pure Appl. Chem. (2001) 73(9):1445-1458.	PDF
S. Filipek, K. Krzysko, M.K. Kalinowski	The Influence of Structural Effects on the Complexing Ability of Crown Ethers. III. Rubidium Complexes Formed by the Ligands of 18C6 Type	Polish J. Chem. (2001) 75:1887-1893.

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July 2023.

GS-SMD web server
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Publication in Nucleic Acids Research 2023 Web server issue.

April 2023.

Homology Modeling book edited by S.Filipek

August 2022.

COGRIMEN

Our new Coarse-Grained Method for Modeling of Membrane Proteins in Implicit Environments.

June 2021.

GPCRsignal

Our new service GPCRsignal was recently published in NAR 2021, W1.