Journal papers

  1. K. Zięba, C. Czaplewski, A. Liwo, G. Graziano. Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models. Phys. Chem. Chem. Phys., 2020,
    DOI: 10.1039/c9cp06627f (Early View)

  2. A. 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. Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. J. Chem. Inf. Model., 2020,
    DOI: 10.1021/acs.jcim.9b00864 (Early View)

  3. A. Liwo, C. Czaplewski. 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. J. Chem. Phys., 2020, 152, 054902
    DOI: 10.1063/1.5138991

  4. J. Eduardo Fajardo, Rojan Shrestha, Nelson Gil, Adam Belsom, Silvia N. Crivelli, Cezary Czaplewski, Krzysztof Fidelis, Sergei Grudinin, Mikhail Karasikov, Agnieszka S. Karczyńska, Andriy Kryshtafovych, Alexander Leitner, Adam Liwo, Emilia A. Lubecka, Bohdan Monastyrskyy, Guillaume Pages, Juri Rappsilber, Adam K. Sieradzan, Celina Sikorska, Esben Trabjerg, Andras Fiser. Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. Proteins: Struct. Func. Bioinf., 2019, 87, 1200-1221
    DOI: 10.1002/prot.25816

  5. E. A. Lubecka, A. S. Karczyńska, A. G. Lipska, A. K. Sieradzan, K. Zięba, 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. Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. J. Molec. Graphics Modeling, 2019, 92, 154-166
    DOI: 10.1016/j.jmgm.2019.07.013

  6. A. Liwo, A. K. Sieradzan, A. G. Lipska, C. Czaplewski, I. Joung, W. Żmudzińska, A. Hałabis, S. Ołdziej. 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. J. Chem. Phys., 2019, 150, 155104
    DOI: 10.1063/1.5093015

  7. E. Lubecka, A. Liwo. Use of contact-distance restraints in the prediction of protein structures with the UNRES force field. J. Comput. Chem., 2019, 40, 2164-2178
    DOI: 10.1002/jcc.25847

  8. E. Lubecka, A. K. Sieradzan, C. Czaplewski, P. Krupa, A. Liwo. High performance computing with coarse grained model of biological macromolecules. Supercomputing Frontiers and Innovations, 2018, 5, 63-67
    DOI: 10.14529/jsfi180206.

  9. C. Czaplewski, A. Karczyńska, A.K. Sieradzan, A. Liwo. UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. Nucleic Acids Research, 2018, 46, W304-W309
    DOI: 10.1093/nar/gky328

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