Publications since 2001

(names in bold are from Biomodeling Group)

updated: July 2019

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
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 2019, in press
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) 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
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
C. Roos, L. Kai, S. Haberstock, D. Proverbio, U. Ghoshdastider, Y. Ma, S. Filipek, X. Wang, V. Dötsch, F. Bernhard High-level cell-free production of membrane proteins with nanodiscs Methods Mol. Biol. (2014) 1118, 109-130. 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. 1118, 2014.
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. Open access
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. Open access
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 Open access
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. Open access
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. Open access
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 (2012) J. Chem. Inf. Model. 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 (2012) FEBS Lett. 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 (2012) Curr. Med. Chem. 19, 1090-1109. Open access
W. Pulawski, U. Ghoshdastider, V. Andrisano, S. Filipek Ubiquitous Amyloids (2012) Appl. Biochem. Biotech. 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 (2012) Method. Enzymol. 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 (2011) Adv. Mat. Lett. 2, 100-105.
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 (2011) Mater. Today 14, 360-365.
B. Jastrzebska, A. Debinski, S. Filipek, K. Palczewski Role of Membrane Integrity on G protein-coupled Receptors: Rhodopsin Stability and Function (2011) Prog. Lipid Res. 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 (2011) J. Mol. Model. 17, 2353-2366. DOI
E. Kilanczyk, S. Filipek, A. Filipek ERK1/2 is dephosphorylated by a novel phosphatase - CacyBP/SIP (2011) Biochem. Biophys. Res. Commun., 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 (2011) Structure 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 (2011) J. Mol. Model. 17, 1467-1472. DOI
P. Somasundaran, S. Viswanathan, M. Chin, S. Filipek, V. Renugopalakrishnan Proteins Immobilized on Surfaces (2010) J. Surface Sci. Technol. 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 (2010) Proc. Natl. Acad. Sci. USA, 107:9644-9649. DOI
Suppl. material
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 (2010) Biochim. Biophys. Acta – Mol. Cell Res., 1803:575-583. DOI
M. Kolinski, S. Filipek Structurally similar pair of agonist and antagonist of kappa opioid receptor studied by molecular dynamics simulations (2010) J. Mol. Model., 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 (2009) TOSBJ, 3:51-63. Open access
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 (2009) Biochemistry, 48:4294-4304. DOI
E. Kilanczyk, S. Filipek, B. Jastrzebska, A. Filipek CacyBP/SIP binds ERK1/2 and affects transcriptional activity of Elk-1 (2009) Biochem. Biophys. Res. Commun., 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 (2009) Biochim. Biophys. Acta – Mol. Cell Res., 1793:1078-1085. DOI
S. Filipek Bioinformatyka strukturalna białek transbłonowych (2009) Kosmos, 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 (2009) J. Phys. Chem. C, 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 (2009) J. Nanosci. Nanotechnol., 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 (2009) J. Nanosci. Nanotechnol., 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 (2009) H.S. Nalwa ed., American Scientific Publishers, Valencia, CA, USA, pp. 155-178.
M. Kolinski, S. Filipek Molecular Dynamics of mu Opioid Receptor Complexes with Agonists and Antagonists (2008) TOSBJ, 2:8-20. Open access
R. Stephen, S. Filipek, K. Palczewski, M.C. Sousa Ca(2+)-dependent Regulation of Phototransduction (2008) Photochem. Photobiol., 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 (2008) Lab. Invest., 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 (2008) ChemMedChem, 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 (2007) Exp. Neurol., 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 (2007) Proc. Natl. Acad. Sci. USA, 104: 13732-13737. DOI
K.A. Krzysko, M. Kolinski, S. Filipek, Molecular modelling of the complex of oligomeric rhodopsin and its G protein (2007) J. Phys.: Condens. Matter, 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 (2007) J. Biol. Chem., 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 (2006) J. Neurochem., 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 (2006) Biochim. Biophys. Acta - Biomembranes, 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 (2006) J. Biol. Chem., 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 (2006) J. Mol. Biol., 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 (2006) Exp. Neurol., 200:82-88. DOI
A. Modzelewska, S. Filipek, K. Palczewski, P.S.-H. Park Arrestin interaction with rhodopsin: conceptual models (2006) Cell Biochem. Biophys., 46:1-15. DOI
S. Filipek, A. Modzelewska chapter Molecular Modelling of Membrane Proteins, in Structural Genomics on Membrane Proteins (2006) K.H. Lundstrom ed., Taylor and Francis, New York, pp. 331-348.
J.S. Jaworski, M. Cembor, M. Kolinski Electrostatic model of bond dissociation energies in polyhalogen methanes (2006) J. Phys. Org. Chem., 19:276-280. DOI
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 (2005) J. Mol. Model., 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) (2005) Invest. Ophth. Vis. Sci., 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 (2004) Biochemistry, 43: 15643-15656. DOI
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D. Fotiadis, Y. Liang, S. Filipek, D.A. Saperstein, A. Engel, K. Palczewski The G protein-coupled receptor rhodopsin in the native membrane (2004) FEBS Lett., 564:281-288. DOI
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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 (2004) Photochem. Photobiol. Sci., 3:628-638. DOI
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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 (2004) J. Biol. Chem., 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 (2004) J. Biol. Chem., 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 (2004) J. Biol. Chem., 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 (2004) Mol. Membr. Biol., 21:435-446. DOI
C. Zekanowski, D. Religa, C. Graff, S. Filipek, J. Kuznicki Genetic aspects of Alzheimer's disease (2004) Acta Neurobiol. Exp., 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) (2004) J. Mol. Evol., 59:204-217. DOI
D. Fotiadis, Y. Liang, S. Filipek, D.A. Saperstein, A. Engel, K. Palczewski Is rhodopsin dimeric in native rods? Reply (2003) Nature, 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 (2003) Nature, 421:127-128. DOI
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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 (2003) J. Biol. Chem., 278: 21655-21662. DOI
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T. Mirzadegan, G. Benko, S. Filipek, K. Palczewski Sequence Analyses of G-Protein-Coupled Receptors: Similarities to Rhodopsin (2003) Biochemistry-US, 42: 2759-2767. DOI
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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 (2003) J. Biol. Chem., 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 (2003) Annu. Rev. Biophys. Biomol. Struct., 32:375-397. DOI
S. Filipek, R.E. Stenkamp, D.C. Teller, K. Palczewski G Protein-Coupled Receptor Rhodopsin: A Prospectus (2003) Annu. Rev. Physiol., 65:851-879. DOI
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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 (2003) Proc. Natl. Acad. Sci. USA, 100:2290-2295. DOI
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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 (2003) J. Neurochem., 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 (2002) J. Biol. Chem., 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 (2002) Biochim. Biophys. Acta - Biomembranes, 1565:168-182. DOI
F. Haeseleer, Y. Imanishi, I. Sokal, S. Filipek, K. Palczewski Calcium-Binding Proteins: Intracellular Sensors from the Calmodulin Superfamily (2002) Biochem. Biophys. Res. Commun., 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 (2001) J. Biol. Chem., 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 (2001) J. Biol. Chem., 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-HT1A and 5-HT2A Serotonin Receptors (2001) Bioorg. Med. Chem., 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 (2001) Pure Appl. Chem., 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 (2001) Polish J. Chem., 75:1887-1893.

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