Publikacje Naukowe
Structural dynamics of the TPR domain of the peroxisomal cargo receptor Pex5 in Trypanosoma M. Banasik, V. Napolitano, A. Blat, K. Abdulkarim, J. Plewka, C. Czaplewski, A. Giełdoń, M. Kozak, B. Wladyka, G. Popowicz, G. Dubin, International Journal of Biological Macromolecules 2024, 280, 135510
Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution. ŁJ Dziadek, AK Sieradzan, C Czaplewski, M Zalewski, F Banaś, M Toczek, W Nisterenko, S Grudinin, A Liwo, A Giełdoń, Journal of Chemical Theory and Computation 2024, 20 (17), 7667-7681
Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems. KM Ocetkiewicz, C Czaplewski, H Krawczyk, AG Lipska, A Liwo, J Proficz, AK Sieradzan, P Czarnul, Computer Physics Communications 2024, 298, 109112
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures. M Lesniewski, M Pyrka, C Czaplewski, NT Co, Y Jiang, Z Gong, C Tang, A Liwo, Journal of Chemical Information and Modeling 2024, 64 (4), 1377-1393
Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size-and timescales. C Czaplewski, P Czarnul, H Krawczyk, AG Lipska, EA Lubecka, KM Ocetkiewicz, J Proficz, AK Sieradzan, R Slusarz, A Liwo, Biophysical Journal 2024, 123 (3), 422a
Exploring the inhibitory potential of in silico-designed small peptides on Helicobacter pylori Hp0231 (DsbK), a periplasmic oxidoreductase involved in disulfide. P Roszczenko-Jasińska, A Giełdoń, D Mazur, M Spodzieja, M Plichta, C Czaplewski, W Bal, EK Jagusztyn-Krynicka, D Bartosik, Frontiers in Molecular Biosciences 2024, 10, 1335704
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment. Marc F Lensink, Guillaume Brysbaert, Nessim Raouraoua, Paul A Bates, Marco Giulini, Rodrigo V Honorato, Charlotte van Noort, Joao MC Teixeira, Alexandre MJJ Bonvin, Ren Kong, Hang Shi, Xufeng Lu, Shan Chang, Jian Liu, Zhiye Guo, Xiao Chen, Alex Morehead, Raj S Roy, Tianqi Wu, Nabin Giri, Farhan Quadir, Chen Chen, Jianlin Cheng, Carlos A Del Carpio, Eichiro Ichiishi, Luis A Rodriguez‐Lumbreras, Juan Fernandez‐Recio, Ameya Harmalkar, Lee‐Shin Chu, Sam Canner, Rituparna Smanta, Jeffrey J Gray, Hao Li, Peicong Lin, Jiahua He, Huanyu Tao, Sheng‐You Huang, Jorge Roel‐Touris, Brian Jimenez‐Garcia, Charles W Christoffer, Anika J Jain, Yuki Kagaya, Harini Kannan, Tsukasa Nakamura, Genki Terashi, Jacob C Verburgt, Yuanyuan Zhang, Zicong Zhang, Hayato Fujuta, Masakazu Sekijima, Daisuke Kihara, Omeir Khan, Sergei Kotelnikov, Usman Ghani, Dzmitry Padhorny, Dmitri Beglov, Sandor Vajda, Dima Kozakov, Surendra S Negi, Tiziana Ricciardelli, Didier Barradas‐Bautista, Zhen Cao, Mohit Chawla, Luigi Cavallo, Romina Oliva, Rui Yin, Melyssa Cheung, Johnathan D Guest, Jessica Lee, Brian G Pierce, Ben Shor, Tomer Cohen, Matan Halfon, Dina Schneidman‐Duhovny, Shaowen Zhu, Rujie Yin, Yuanfei Sun, Yang Shen, Martyna Maszota‐Zieleniak, Krzysztof K Bojarski, Emilia A Lubecka, Mateusz Marcisz, Annemarie Danielsson, Lukasz Dziadek, Margrethe Gaardlos, Artur Gieldon, Adam Liwo, Sergey A Samsonov, Rafal Slusarz, Karolina Zieba, Adam K Sieradzan, Cezary Czaplewski, Shinpei Kobayashi, Yuta Miyakawa, Yasuomi Kiyota, Mayuko Takeda‐Shitaka, Kliment Olechnovic, Lukas Valancauskas, Justas Dapkunas, Ceslovas Venclovas, Bjorn Wallner, Lin Yang, Chengyu Hou, Xiaodong He, Shuai Guo, Shenda Jiang, Xiaoliang Ma, Rui Duan, Liming Qui, Xianjin Xu, Xiaoqin Zou, Sameer Velankar, Shoshana J Wodak, Proteins: Structure, Function, and Bioinformatics 2023, 91 (12), 1658-1683
Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches. AG Lipska, AK Sieradzan, S Atmaca, C Czaplewski, A Liwo, Journal of Physical Chemistry Letters 2023, 14 (44), 9824-9833
Pragmatic coarse-graining of proteins: models and applications L Borges-Araújo, I Patmanidis, AP Singh, LHS Santos, AK Sieradzan, S Vanni, C Czaplewski, S Pantano, W Shinoda, L Monticelli, A Liwo, SJ Marrink, PCT Souza, Journal of Chemical Theory and Computation 2023, 19 (20), 7112-7135
Long‐time scale simulations of virus‐like particles from three human‐norovirus strains. AG Lipska, AK Sieradzan, C Czaplewski, AD Lipińska, KM Ocetkiewicz, Jerzy Proficz, P Czarnul, H Krawczyk, A Liwo, Journal of Computational Chemistry 2023, 44 (16), 1470-1483
Long-time dynamics of selected molecular-motor components using a physics-based coarse-grained approach. A Liwo, M Pyrka, C Czaplewski, X Peng, AJ Niemi, Biomolecules 2023, 13 (6), 941
UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time-and size-scales. KM Ocetkiewicz, C Czaplewski, H Krawczyk, AG Lipska, A Liwo, J Proficz, AK Sieradzan, P Czarnul, Bioinformatics 2023, 39 (6), btad391
Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins. AK Sieradzan, J Sans‐Duñó, EA Lubecka, C Czaplewski, AG Lipska, H Leszczyński, KM Ocetkiewicz, J Proficz, P Czarnul, H Krawczyk, A Liwo, Journal of Computational Chemistry 2023, 44 (4), 602-625
N-Terminally Lipidated Sialorphin Analogs—Synthesis, Molecular Modeling, In Vitro Effect on Enkephalins Degradation by NEP and Treatment of Intestinal Inflammation in Mice. M. Sobocińska, J. Fichna, A. Giełdoń, P. Skowron, E. Kamysz, Int. J. Mol. Sci. 2022, 23(22), 14450
Low-molecular pyrazine-based DNA binders: Physicochemical and antimicrobial properties. P Mech-Warda, A Giełdoń, A Kawiak, N Maciejewska, M Olszewski, M Makowski, A Chylewska, Molecules 2022, 27 (12), 3704
Peptidomimetics Based on C-Terminus of Blm10 Stimulate Human 20S Proteasome Activity and Promote Degradation of Proteins. K Cekała, K Trepczyk, D Sowik, P Karpowicz, A Giełdoń, J Witkowska, M Giżyńska, E Jankowska, E Wieczerzak, Biomolecules 2022, 12 (6), 777
Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions R Ślusarz, EA Lubecka, C Czaplewski, A Liwo, Frontiers in Molecular Biosciences 2022, 9, 1071428
Prediction of aggregation of biologically-active peptides with the UNRES coarse-grained model. I Biskupek, C Czaplewski, J Sawicka, E Iłowska, M Dzierżyńska, S Rodziewicz-Motowidło, A Liwo, Biomolecules 2022, 12 (8), 1140
Theoretical investigation of the coronavirus SARS-CoV-2 (COVID-19) infection mechanism and selectivity. I Biskupek, A Sieradzan, C Czaplewski, A Liwo, A Lesner, A Giełdoń, Molecules 2022, 27 (7), 2080
Influence of temperature and salt concentration on the hydrophobic interactions of adamantane and hexane M Bogunia, A Liwo, C Czaplewski, J Makowska, A Giełdoń, M Makowski, Journal of Physical Chemistry B 2022, 126 (3), 634-642
Modeling the structure, dynamics, and transformations of proteins with the UNRES force field. AK Sieradzan, C Czaplewski, P Krupa, MA Mozolewska, AS Karczyńska, AG Lipska, EA Lubecka, E Gołaś, T Wirecki, M Makowski, S Ołdziej, A Liwo, Protein folding: Methods and protocols 2022, 399-416
Physics-Based Coarse-Grained Modeling in Bio-and Nanochemistry. A Liwo, AK Sieradzan, AS Karczyńska, EA Lubecka, SA Samsonov, C Czaplewski, P Krupa, M Mozolewska, Practical Aspects of Computational Chemistry 2021, V, 31-69
Recent developments in data-assisted modeling of flexible proteins. C Czaplewski, Z Gong, EA Lubecka, K Xue, C Tang, A Liwo, Frontiers in Molecular Biosciences 2021, 8, 765562
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment. Marc F Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael AG Chaleil, Tereza Clarence, Paul A Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka G Lipska, Adam Liwo, Emilia A Lubecka, Martyna Maszota‐Zieleniak, Adam K Sieradzan, Rafał Ślusarz, Patryk A Wesołowski, Karolina Zięba, Carlos A Del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J Gray, Alexandre MJJ Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jiménez‐García, Panagiotis I Koukos, Siri Van Keulen, Charlotte W Van Noort, Manon Réau, Jorge Roel‐Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A Rodríguez‐Lumbreras, Juan Fernandez‐Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng‐you Huang, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G Pierce, Didier Barradas‐Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda‐Shitaka, Petras J Kundrotas, Amar Singh, Ilya A Vakser, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J Wodak, Proteins: Structure, Function, and Bioinformatics 2021, 89 (12), 1800-1823
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment. A Antoniak, I Biskupek, KK Bojarski, C Czaplewski, A Giełdoń, M Kogut, MM Kogut, P Krupa, AG Lipska, A Liwo, EA Lubecka, M Marcisz, M Maszota-Zieleniak, SA Samsonov, AK Sieradzan, MJ Ślusarz, R Ślusarz, PA Wesołowski, K Ziȩba, Journal of Molecular Graphics and Modelling 2021, 108, 108008
Theoretical investigation of the structural insights of the interactions of γ-Fe2O3 nanoparticle with (EMIM TFSI) ionic liquid. AK Sieradzan, C Czaplewski, A Bielicka-Gieldon, M Bobrowski, A Gieldon, Journal of Molecular Liquids 2021, 340, 117198
Theory and practice of coarse-grained molecular dynamics of biologically important systems A Liwo, C Czaplewski, AK Sieradzan, AG Lipska, SA Samsonov, RK Murarka, Biomolecules 2021, 11 (9), 1347
UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations. P Krupa, AS Karczyńska, MA Mozolewska, A Liwo, C Czaplewski, Bioinformatics 2021, 37 (11), 1613-1615
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers. A. Liwo, C. Czaplewski, A.K. Sieradzan, E.A. Lubecka, A.G. Lipska, Ł. Golon, A. Karczyńska, P. Krupa, M.A. Mozolewska, M. Makowski, R. Ganzynkowicz, A. Giełdoń, M. Maciejczyk, Progress in Molecular Biology and Translational Science 2020, 170, 73-122
A peptidomimetic fluorescent probe to detect the trypsin β2 subunit of the human 20S proteasome. M. Wysocka, A. Romanowska, N. Gruba, M. Michalska , A. Giełdoń, A. Lesner, Int. J. Mol. Sci. 2020, 21, 1-16
Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models. K. Zięba, C. Czaplewski, A. Liwo, G. Graziano, Phys. Chem. Chem. Phys. 2020, 22, 4758-4771
Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13. A.S. Karczyńska, K. Zięba, U. Uciechowska, M.A. Mozolewska, P. Krupa, E.A. Lubecka, A.G. Lipska, C. Sikorska, S.A. Samsonov, A.K. Sieradzan, A. Giełdoń, A. Liwo, R. Ślusarz, M. Ślusarz, J. Lee, K. Joo, C. Czaplewski, J. Chem. Inf. Model. 2020, 60, 1844-1864
Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins. A Liwo, C Czaplewski, J. Chem. Phys. 2020, 152, 054902.
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. M.F Lensink, G. Brysbaert, N. Nadzirin, S. Velankar, R.A.G. Chaleil, T. Gerguri, P.A. Bates, E. Laine, A. Carbone, S. Grudinin, R. Kong, R. Liu, X. Xu, H. Shi, S. Chang, M. Eisenstein, A. Karczynska, C. Czaplewski, E. Lubecka, A. Lipska, P. Krupa, M. Mozolewska, Ł. Golon, S. Samsonov, A. Liwo, S. Crivelli, G. Pagès, M. Karasikov, M. Kadukova, Y. Yan, S. Huang, M. Rosell, L.A. Rodríguez‐Lumbreras, M. Romero‐Durana, L. Díaz‐Bueno, J. Fernandez‐Recio, C. Christoffer, G. Terashi, W. Shin, T. Aderinwale, S.R.M.V. Subraman, D. Kihara, D. Kozakov, S. Vajda, K. Porter, D. Padhorny, I. Desta, D. Beglov, M. Ignatov, S. Kotelnikov, I.H. Moal, D.W. Ritchie, I.C. de Beauchêne, B. Maigret, M.D. Devignes, M.E.R. Echartea, D. Barradas‐Bautista, Z. Cao, L. Cavallo, R. Oliva, Y. Cao, Y. Shen, M. Baek, T. Park, H. Woo, C. Seok, M. Braitbard, L. Bitton, D. Scheidman‐Duhovny, J. Dapkūnas, K. Olechnovič, Č. Venclovas, P.J. Kundrotas, S. Belkin, D. Chakravarty, V.D. Badal, I.A. Vakser, T. Vreven, S. Vangaveti, T. Borrman, Z. Weng, J.D. Guest, R. Gowthaman, B.G. Pierce, X. Xu, R. Duan, L. Qiu, J. Hou, B. Ryan Merideth, Z. Ma, J. Cheng, X. Zou, P.I. Koukos, J. Roel‐Touris, F. Ambrosetti, C. Geng, J. Schaarschmidt, M.E. Trellet, A.S.J. Melquiond, L. Xue, B. Jiménez‐García, C.W. van Noort, R.V. Honorato, A.M.J.J. Bonvin, S.J. Wodak, Proteins 2019, 87, 1200-1221
Introduction of phosphorylated residues into the UNRES coarse-grained model: toward modeling of signaling processes A. Sieradzan, M. Bogunia, P. Mech, R. Ganzynkowicz, A. Giełdoń, A. Liwo, M. Makowski, J. Phys. Chem. B 2019, 123, 5721-5729
1-substituted sialorphin analogues - synthesis, molecular modelling and in vitro effect on enkephalins degradation by NEP M. Sobocińska, A. Giełdoń, J. Fichna, E. Kamysz, Amino Acids 2019, 51, 1201-1207
Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C. B. Korkmaz, A. Lesner, M. Wysocka, A. Giełdoń, M. Håkansson, F. Gauthier, D.T. Logan, D. Jenne, C. Lauritzen, J. Pedersen, Biochem. Pharmacol. 2019, 164, 349-367
Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. J.E. Fajardo, R. Shrestha, N. Gil, A. Belsom, S.N. Crivelli, C. Czaplewski, K. Fidelis, S. Grudinin, M. Karasikov, A.S. Karczyńska, A. Kryshtafovych, A. Leitner, A. Liwo, E.A. Lubecka, B. Monastyrskyy, G. Pagès, J. Rappsilber, A.K. Sieradzan, C. Sikorska, E. Trabjerg, A. Fiser, Proteins 2019, 87, 1283-1297
Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. E.A. Lubecka, A.S. Karczyńska, A.G. Lipska, A.K. Sieradzan, K. Ziȩba, C. Sikorska, U. Uciechowska, S.A Samsonov, P. Krupa, M.A. Mozolewska, Ł. Golon, A. Giełdoń, C. Czaplewski, R. Ślusarz, M. Ślusarz, S.N. Crivelli, A. Liwo, J. Mol. Graph. Model. 2019, 92, 154-166
Extension of the UNRES coarse-grained force field to membrane proteins in the lipid bilayer. K. Ziȩba, M. Ślusarz, R. Ślusarz, A. Liwo, C. Czaplewski, A.K. Sieradzan, J. Phys. Chem. B 2019, 123, 7829-7839
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. A. Liwo, A.K. Sieradzan, A.G. Lipska, C. Czaplewski, I. Joung, W. Żmudzińska, A. Hałabis, S. Ołdziej, J. Chem. Phys. 2019, 150, 155104
Processing and maturation of cathepsin C zymogen: a biochemical and molecular modeling analysis. A.S. Lamort, Y. Hamon, C. Czaplewski, A. Giełdoń, S. Seren, L. Coquet, F. Lecaille, A. Lesner, G. Lalmanach, F. Gauthier, D. Jenne, B. Korkmaz, Int. J. Mol. Sci. 2019, 20, 4747
Formation of secondary and supersecondary structure of proteins as a result of coupling between local and backbone-electrostatic interactions: a view through cluster-cumulant scope. A. Liwo, A.K. Sieradzan, C. Czaplewski, In: Kister A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 1958. Humana Press, New York, NY, pp. 133-146 (2019).
Use of Coarse-Grained and All-Atom Molecular Dynamics to Study Hsp70 and Hsp40 Chaperone Action, E.I. Golas, M.A. Mozolewska, P. Krupa, C. Czaplewski, H.A. Scheraga, A. Liwo in Frontiers in Structural Biology Vol. 1 edited by M.D. Galigniana, Bentham Publishers, pp 23-46 (2018). ISBN: 978-1-68108-616-3
High performance computing with coarse-grained model of biological macromolecules. E. Lubecka, A. Sieradzan, C. Czaplewski, P. Krupa, A. Liwo, Supercomputing Frontiers and Innovations 2018, 5, 63-75.
Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase, M. J. Grzeszczuk, A. Bak, A. M. Banas, P. Urbanowicz, S. Dunin-Horkawicz, A. Gieldon, C. Czaplewski, A. Liwo, E.K. Jagusztyn-Krynicka, Plos One 2018, 13, e0195358.
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics, C. Czaplewski, A. Karczyńska, A.K Sieradzan, A. Liwo Nucleic Acids Res. 2018, 46, W304-W309.
Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: test with CASP12 targets, A. Karczyńska, M.A. Mozolewska, P. Krupa, A.Giełdoń, K.K. Bojarski, B. Zaborowski, A. Liwo, R. Ślusarz, M. Ślusarz, J. Lee, K. Joo, C. Czaplewski, J. Mol. Graph. Model. 2018, 83, 92-99.
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12, C. Keasar, L. McGuffin, B. Wallner, G. Chopra, B. Adhikari, D. Bhattacharya, L. Blake, L. Bortot, R. Cao, B.K. Dhanasekaran, I. Dimas, R. Faccioli, E. Faraggi, R. Ganzynkowicz, S. Ghosh, S. Ghosh, A. Gieldon, L. Golon, Y. He, L. Heo, J. Hou, M. Khan, F. Khatib, G. Khoury, C. Kieslich, D. Kim, P. Krupa, G.R. Lee, H. Li, J. Li, A. Lipska, A. Liwo, A. Maghrabi, M. Mirdita, S. Mirzaei, M. Mozolewska, M. Onel, S. Ovchinnikov, A. Shah, U. Shah, T. Sidi, A. Sieradzan, M. Ślusarz, R. Slusarz, J. Smadbeck, P. Tamamis, N. Trieber, T. Wirecki, Y. Yin, Y. Zhang, J. Bacardit, M. Baranowski, N. Chapman, S. Cooper, Al. Defelicibus, J. Flatten, B. Koepnick, Z. Popović, B. Zaborowski, D. Baker, J. Cheng, C. Czaplewski, A. Delbem, C. Floudas, A. Kloczkowski, S. Ołdziej, M. Levitt, H. Scheraga, C. Seok, J. Söding, S. Vishveshwara, D. Xu, and S. Crivelli Scientific Reports 2018, 8, 9939.
Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information, A. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, A. Liwo, C. Czaplewski, Proteins: Struct. Funct. Bioinf. 2018, 86, 228-239. CASP12 special issue.
Acid-base properties of 3-[2-(n-quinolinyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies, A. Lewandowska, D. Wroblewski, K. Guzow, M. Milewska, C. Czaplewski, W. Wiczk J. Photochem. Photobiol. A - Chemistry 2018, 353, 191-199.
Biochemical properties of the HtrA homolog from bacterium Stenotrophomonas maltophilia, U. Zarzecka, A. Modrak-Wojcik, M. Bayassi, M. Szewczyk, A. Gieldon, A. Lesner, T. Koper, A. Bzowska, M. Sanguinetti, S. Backert, B. Lipinska, J. Skorko-Glonek, Int. J. Biol. Macromol. 2018, 109, 992-1005.
Microscopic Physics-Based Models of Proteins and Nucleic Acids: UNRES and NARES, M. Baranowski, C. Czaplewski, E. Golas, Y. He, D. Jagiela, P. Krupa, A. Liwo, G.G. Maisuradze, M. Makowski, M.A. Mozolewska, A. Niadzvedtski, A.J. Niemi, S. Rackovsky, R. Slusarz, A.K. Sieradzan, S. Oldziej, T. Wirecki, Y. Yin, B. Zaborowski, H.A. Scheraga, in Coarse-Grained Modeling of Biomolecules (Series in Computational Biophysics), edited by G.A. Papoian, CRC Press (2018) pp. 67-120. ISBN 978-1-4665-7606-3
Chemoinformatics methods for studying biomolecules, A. Liwo, C. Czaplewski, S. Ołdziej, B. Zaborowski, D. Jagieła, J. Lee, in Handbook of computational chemistry, edited by J. Leszczyński. Springer (2017) pp. 2183-2199. ISBN 978-3-319-27281-8
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins, A. Karczyńska, C. Czaplewski, P. Krupa, M. Mozolewska, K. Joo, J. Lee, A. Liwo, J. Comput. Chem. 2017, 38, 2730–2746.
Crystal structure of a low molecular weight activator Blm-pep with yeast 20S proteasome – insights into the enzyme activation mechanism, J. Witkowska, M. Giżyńska, P. Grudnik, P. Golik, P. Karpowicz, A. Giełdoń, G. Dubin, E. Jankowska, Sci. Rep. 2017, 7, 6177.
Rapid insight into C60 influence on biological functions of protein, A. Giełdoń, M. Witt, A. Gajewicz, T. Puzyn, Struct. Chem. 2017, 28, 1775-1788.
Selection of effective HTRA3 activators using combinatorial chemistry, M. Wysocka, K. Sychowska, N. Gruba, Ł. Winiarski, M. Skoreński, M. Psurski, J. Makowska, A. Giełdoń, T. Wenta, M. Jarząb, P. Glaza, J. Zdancewicz, M. Sieńczyk, B. Lipińska, A. Lesner., ACS Comb. Sci. 2017, 19, 565-573.
Structural insights into the activation mechanisms of human HtrA serine proteases, D. Żurawa-Janicka, T. Wenta, M. Jarząb, J. Skórko-Glonek, P. Glaza, A. Giełdoń, J. Ciarkowski, B. Lipińska, Arch. Biochem. Biophys. 2017, 621, 6-23.
Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation, M. Szyszkowska, C. Czaplewski, W. Wiczk, J. Mol. Structure 2017, 1138, 81-89.
Polymerization of chloro-p-xylylenes, quantum-chemical study, C. Czaplewski, K. Smalara, A. Giełdoń, M. Bobrowski, J.Mol.Model. 2017, 23, 40.
Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids, A. Giełdoń, M. Bobrowski, A. Bielicka-Giełdoń, C. Czaplewski, J.Mol.Liq. 2017, 225, 467–474.
Role of the sulfur to α-carbon thioether bridges in thurincin H, M.A. Mozolewska, A.K. Sieradzan, A. Niadzvedstki, C. Czaplewski, A. Liwo, P. Krupa, J. Biomol. Struct. Dyn. 2017, 35, 2868-2879.
Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. M. Mozolewska, P. Krupa, B. Zaborowski, A. Liwo, J. Lee, K. Joo, C. Czaplewski, J. Chem. Inf. Model. 2016, 56, 2263-2279.
PEGylated substrates of NSP4 protease : a tool to study protease specificity M. Wysocka, N. Gruba, R. Grzywa, A. Giełdoń, R. Bąchor, K. Brzozowski, M. Sieńczyk, J. Dieter, Z. Szewczuk, K. Rolka, A. Lesner. Scientific Reports 2016, 6, art. no. 22856, 1-11
Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction A.G. Lipska, S.R. Seidman, A.K. Sieradzan, A. Giełdoń, A. Liwo, H.A. Scheraga. J. Chem. Phys. 2016, 144, art.no.184110, 1-11
Intra- and intersubunit changes accompanying thermal activation of the HtrA2(Omi) protease homotrimer M. Jarząb, T. Wenta, D. Żurawa-Janicka, A. Polit, A. Giełdoń, M. Wysocka, P. Glaza, J. Skórko-Glonek, J. Ciarkowski, A. Lesner, B. Lipińska. Biochimica et Biophysica Acta. Proteins and Proteomics 2016, 1864, 283-296
Distinct 3D architecture and dynamics of the human HtrA2(Omi) protease and its mutated variants A. Giełdoń, D. Żurawa-Janicka, M. Jarząb, T. Wenta, P. Golik, G. Dubin, B. Lipińska, J. Ciarkowski. PLoS One 2016, 11, e.0161526, 1-19
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. P. Krupa, M.A. Mozolewska, M. Wiśniewska, Y. Yin, Y. He, A.K. Sieradzan, R. Ganzynkowicz, A.G. Lipska, A. Karczyńska, M. Ślusarz, R. Ślusarz, A. Giełdoń, C. Czaplewski, D. Jagieła, B. Zaborowski, H.A. Scheraga, A. Liwo, Bioinformatics 2016, 32, 3270–3278
Bladder cancer detection using a peptide substrate of the 20S proteasome. N. Gruba, M. Wysocka, M. Brzezińska, D. Dębowski, M.Sieńczyk, E. Gorodkiewicz, T. Guszcz, C. Czaplewski, K. Rolka and A. Lesner, FEBS J. 2016, 283, 2929–2948
Temperature-dependent structure-property modeling of viscosity for ionic liquids. M. Barycki, A. Sosnowska, A. Gajewicz, M. Bobrowski, D. Wileńska, P. Skurski, A. Giełdoń, C. Czaplewski, S. Uhl, E. Laux, T. Journot, L. Jeandupeux, H. Keppner, T. Puzyn. Fluid Phase Equilibria 2016, 427, 9-17
Photophysical properties of symmetrically substituted diarylacetylenes and diarylbuta-1,3-diynes I. Bylińska, M. Wierzbicka, C. Czaplewski, Wiesław Wiczk. Photochem. Photobiol. Sci. 2016, 15, 45-56
A maximum-likelihood approach to force-field calibration. B. Zaborowski, D. Jagieła, C. Czaplewski, A. Hałabis, A. Lewandowska, W. Żmudzińska, S. Ołdziej, A. Karczyńska, C. Omieczynski, T. Wirecki, A. Liwo. J. Chem. Inf. Model. 2015, 55, 2050-2070
Common functionally important motions of the nucleotide-binding domain of Hsp70 E.I. Gołaś, C. Czaplewski, H.A. Scheraga, A. Liwo. Proteins: Struct. Funct. Bioinf. 2015, 83, 282-299
Experimental and theoretical studies of spectroscopic properties of simple symmetrically substituted diphenylbuta-1,3-diyne derivatives. M. Wierzbicka, I. Bylińska, A. Sikorski, C. Czaplewski, W. Wiczk Photochem Photobiol Sci. 2015, 14, 2251-2260
Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives. M. Wierzbicka, I. Bylińska, C. Czaplewski, W. Wiczk RSC Adv. 2015, 5, 29294-29303
Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the United Residue (UNRES) force field for protein simulations A.K. Sieradzan, P. Krupa, H.A. Scheraga, A. Liwo, C. Czaplewski. J. Chem. Theory. Comput. 2015, 11, 817-831
Prediction of protein structure by template-based modeling combined with the UNRES force field P. Krupa, M.A. Mozolewska, K. Joo, J. Lee, C. Czaplewski, A. Liwo. J. Chem. Inf. Model. 2015, 55, 1271-1281
RASMOL AB - New functionalities in the program for structure analysis M. Pikora, A. Giełdoń. Acta Biochim. Pol 2015, 62, 629-631
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions A. Liwo, M. Baranowski, C. Czaplewski, E. Gołaś, Y. He, D. Jagieła, P. Krupa, M. Maciejczyk, M. Makowski, M.A. Mozolewska, A. Niadzvedtski, S. Ołdziej, H.A. Scheraga, A.K. Sieradzan, R. Ślusarz, T. Wirecki, Y. Yin, B. Zaborowski. J. Mol. Model. 2014, 20, 1-15
Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements R. Zhou, G.G. Maisuradze, D. Suñol, T. Todorovski, M.J. Macias, Y. Xiao, H.A. Scheraga, C. Czaplewski, A. Liwo. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 18243-18248
Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer E.I. Gołaś, C. Czaplewski. Biopolymers. 2014, 101, 915-923
Solvatochromic studies of pull-push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit I. Bylińska, M. Wierzbicka, C. Czaplewski, W. Wiczk, RSC Adv. 2014, 4, 48783-48795
Towards mechanisms of nanotoxicity - interaction of gold nanoparticles with proteins and DNA P. Krupa, M.A. Mozolewska, B. Rasulev, C. Czaplewski, J. Leszczynski, TASK Quarterly. 2014, 18, 337-341
The LA loop as an important regulatory element of the HtrA (DegP) protease from Escherichia coli : structural and functional studies D. Figaj, A. Giełdoń, A. Polit, A. Sobiecka-Szkatuła, T. Koper, M. Denkiewicz, B. Banecki, A. Lesner, J. Ciarkowski, B. Lipińska, J. Skórko-Glonek. J. Biol. Chem. 2014, 289, 15880-15893
Preliminary studies on trigonelline as potential anti-Alzheimer disease agent : determination by hydrophilic interaction liquid chromatography and modeling of interactions with beta-amyloid. J. Makowska, D. Szczesny, A. Lichucka, A. Giełdoń, L. Chmurzyński, R. Kaliszan. J. Chromatogr. B. 2014, 968, 101-104
Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states. P. Krupa, A.K. Sieradzan, S. Rackovsky, M. Baranowski, S. Ołdziej, H.A. Scheraga, A. Liwo, C. Czaplewski, J. Chem. Theory. Comput. 2013, 9, 4620-4632
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Y. He, M.A. Mozolewska, P. Krupa, A.K. Sieradzan, T.K. Wirecki, A. Liwo A, K. Kachlishvili, S. Rackovsky, D. Jagiela, R. Ślusarz, C. Czaplewski, S. Ołdziej, H.A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 14936-14941.
Acid-base properties of 3-[2-(pyridyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state : experimental and theoretical studies A. Lewandowska, K. Guzow, D. Wróblewski, C. Czaplewski, W. Wiczk, J. Photochem. Photobiol. A Chem. 2013, 258, 10-16
Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives--experimental and theoretical studies. K. Guzow, M. Czerwińska, A. Ceszlak, M. Kozarzewska, M. Szabelski, C. Czaplewski, A. Łukaszewicz, A.A. Kubicki, W. Wiczk, Photochem. Photobiol. Sci. 2013, 12, 284-297.
Temperature-induced changes of HtrA2(Omi) protease activity and structure. D. Zurawa-Janicka, M. Jarzab, A. Polit, J. Skorko-Glonek, A. Lesner, A. Gitlin, A. Gieldon, J. Ciarkowski, P. Glaza, A. Lubomska, B. Lipinska, Cell Stress Chaperones. 2013, 18, 35-51.