LIST OF PUBLICATIONS 13.01.2022

  1. M. Nowacka, S. Ołdziej, C. Czaplewski, J. Ciarkowski, F.M.F. Chen and N. Benoiton, Reaction mechanisms in peptide sythesis 3. An assessment of a mixed anhydride reactivity by means of the molecular orbital AM1 and PM3 methods, Polish J. Chem., 68, 1715-1723 (1994).

  2. C. Czaplewski, B. Lammek and J. Ciarkowski, Conformational constraints emerging in the N,N'-ethylene- and N,N'-propylene-bridged dipeptide units, Polish J. Chem., 68, 2589-2598 (1994).

  3. I.Z. Siemion, P. Stefanowicz, C. Czaplewski and J. Ciarkowski, The β-turn-like conformation of tripeptides with C-terminal proline, Polish J. Chem., 69, 902-911 (1995).

  4. R. Kazmierkiewicz, C. Czaplewski, B. Lammek, J. Ciarkowski and B. Lesyng, Study of the interactions between neurophysin and dipeptide ligand by means of molecular dynamics, J. Mol. Model., 1, 143-149 (1995).

  5. W. Wiczk, L. Łankiewicz, C. Czaplewski, S. Oldziej, K. Stachowiak, A. Michniewicz, A. Liwo, The photophysics of β-homo-Tyrosine and its simple derivatives, J. Photochem. Photobiol. A - Chemistry, 101, 171-181 (1996).

  6. R. Kazmierkiewicz, C. Czaplewski, B. Lammek, J. Ciarkowski, Molecular modeling of the neurophysin I - oxytocin complex, J. Comput.-Aided. Mol. Design, 11, 9-20 (1997).

  7. W. Wiczk, K. Stachowiak, C. Czaplewski, L. Łankiewicz and A. Michniewicz, Photophysical properties of (p-hydroxy)phenylglycine, J. Photochem. Photobiol. A - Chemistry, 102, 189 (1997).

  8. R. Kazmierkiewicz, C. Czaplewski, B. Lammek, J. Ciarkowski, Molecular modeling of the neurophysin II - vasopressin complex, Quantitative Structure-Activity Relationship, 16, 193-200 (1997).

  9. P. Arłukowicz, E. Biernat, J. Ciarkowski, C. Czaplewski, M. Groth, R. Kazmierkiewicz, A. Liwo, K. Maksimiak, M. Nowacka, S. Ołdziej, S. Rodziewicz, E. Wozniak, Molecular simulations with high-performance computers. T.A.S.K. Quarterly, 1, 21 (1997).

  10. R. Kazmierkiewicz, C. Czaplewski, J. Ciarkowski, Elucidation of neurophysin / bioligand interactions from molecular modeling, Acta Biochim. Pol., 44, 453-466 (1997).

  11. A. Liwo, S. Ołdziej, R. Kazmierkiewicz, M. Groth, C. Czaplewski. Design of a knowledge-based force field for off-lattice simulations of protein structure, Acta Biochim. Pol., 44, 527-547 (1997).

  12. W. Wiczk, L. Łankiewicz, C. Czaplewski, S. Ołdziej, K. Stachowiak, A. Michniewicz, B. Micewicz, A. Liwo, The photophysics of β-Tyrosine and its simple derivatives, J. Fluoresc., 7, 257 (1997).

  13. C. Czaplewski, R. Kazmierkiewicz, J. Ciarkowski, P. Herzyk and R. Hubbard, Molecular modeling of the V2 receptor - ligand interactions: A tool toward understanding the mechanism of action of vasopressin and its antagonists, Peptides 1996, Proceedings of the 24th Symposium of the European Peptide Society, Eds. R. Ramage and R. Epten, 319 (1998).

  14. C. Czaplewski, R. Kazmierkiewicz, B. Lammek and J. Ciarkowski, Molecular modeling of the neurophysin I - oxytocin complex, Peptides 1996, Proceedings of the 24th Symposium of the European Peptide Society, Eds. R. Ramage and R. Epten, 531 (1998).

  15. A. Liwo, R. Kazmierkiewicz, C. Czaplewski, M. Groth, S. Ołdziej, R.J. Wawak, S. Rackovsky, M.R. Pincus, H.A. Scheraga. A United-Residue Force Field for Off-Lattice Protein-Structure Simulations. III. Origin of Backbone Hydrogen-Bonding Cooperativity in United-Residue Potentials, J. Comput. Chem., 19, 259-276 (1998).

  16. C. Czaplewski, R. Kazmierkiewicz, J. Ciarkowski, Molecular modeling of the human vasopressin V2 receptor/agonist complex, J. Comput.-Aided. Mol. Design , 12, 275-287 (1998).

  17. S. Rodziewicz, C. Czaplewski, A. Liwo, A. Legowska, K. Klugman, A. Lesner, K. Rolka, Conformation of tachykinin peptides by computer simulation and NMR spectroscopy T.A.S.K. Quarterly, 2, 25 (1998).

  18. C. Czaplewski, Theoretical study of proton-transfer energy surfaces in small water clusters and cubic ice. T.A.S.K. Quarterly, 2, 31 (1998).

  19. C. Czaplewski, R. Kazmierkiewicz, J. Ciarkowski, Molecular modelling of the vasopressin V2 receptor/antagonist interactions Acta Biochim. Pol. , 45, 19-26 (1998).

  20. C. Czaplewski, R. Kazmierkiewicz, J. Ciarkowski, Vasopressin V2 receptor / bioligand interactions, Lett. Peptide Sci, 5, 333-335 (1998).

  21. J. Malicka, M. Groth, C. Czaplewski, A. Liwo, W. Wiczk, L. Łankiewicz, Computer modeling of the solution conformation of cyclic enkephalins, Lett. Peptide Sci., 5, 445-447 (1998).

  22. J. Ciarkowski, C. Czaplewski, R. Kazmierkiewicz, E. Politowska, Receptory sprzężone z białkami G (GPCR): struktura i oddziaływania z bioligandami, Wiadomości Chemiczne, 52, 107 (1998).

  23. J. Ciarkowski, C. Czaplewski and M.Pasenkiewicz-Gierula. Target for majority of drugs: G protein-coupled receptors - their structure and interactions with bioligands, T.A.S.K. Quarterly, 2, 583 (1998).

  24. A. Liwo, J. Pilardy, R. Kazmierkiewicz, R.J. Wawak, M. Groth, C. Czaplewski, S. Ołdziej, H.A. Scheraga. Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods, Theor. Chem. Acc., 101, 16-20 (1999).

  25. R. Kazmierkiewicz, C. Czaplewski, B. Lammek, J. Ciarkowski, Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories, J. Comput.-Aided. Mol. Design , 13, 21-33 (1999).

  26. C. Czaplewski, M.Pasenkiewicz-Gierula and J. Ciarkowski, Molecular dynamics of a vasopressin V2 receptor in a phospholipid bilayer membrane, J. Rec. Signal Trans. Research, 19, 355-367 (1999).

  27. C. Czaplewski, M.Pasenkiewicz-Gierula and J. Ciarkowski, G Protein-Coupled Receptor - bioligand interactions modeled in a phospholipid bilayer, Int. J. Quant. Chem., 73, 61-70 (1999).

  28. C. Czaplewski, Z. Grzonka, M. Jaskólski, F. Kasprzykowski, M. Kozak, E. Politowska, J. Ciarkowski, Binding modes of a new epoxysuccinylpeptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity ? BBA - Protein Struct. Mol. Enzym., 1431, 290-305 (1999).

  29. J. Malicka, M. Groth, C. Czaplewski, A. Liwo, W. Wiczk, Fluorescence decay time distribution analysis of cyclic enkephalin analogues. Influence of the solvents and configuration of amino acids in position 2 and 3 on changes in conformation, Acta Biochim. Pol., 46, 615-629 (1999).

  30. E. Politowska, C. Czaplewski, J. Ciarkowski, Molecular modeling of the oxytocin receptor/bioligand interactions, Acta Biochim. Pol., 46, 581-590 (1999).

  31. D.R. Ripoll, A. Liwo, C. Czaplewski, The ECEPP package for conformational analysis of polypeptides, T.A.S.K. Quarterly, 3, 313-331 (1999).

  32. M. Groth, J. Malicka, C. Czaplewski, S. Ołdziej, L. Łankiewicz, W. Wiczk and A. Liwo Maximum entropy approach to the determination of solution conformation of flexible polypeptide by global conformational analysis and NMR spectroscopy - application to DNS1-c-[D-A2bu2,Trp4,Leu5]enkephalin and DNS1-c-[D-A2bu2,Trp4,D-Leu5]enkephalin, J. Biomol. NMR, 15, 315-330 (1999).

  33. S. Rodziewicz, I. Wirkus-Romanowska, M. Ciurak, H. Miecznikowska, G. Kupryszewski, C. Czaplewski, A. Liwo, K. Rolka Cyclic analogues of proline-rich protein fragments. Part II: Conformational studies using NMR spectroscopy and theoretical conformational analysis, Polish J. Chem., 73, 1697-1710 (1999).

  34. J. Pillardy, R.J. Wawak, Y.A. Arnautova, C. Czaplewski, and H.A. Scheraga, Crystal structure prediction by global optimization as a tool for evaluating potentials; the role of the dipole moment correction term in succesful prediction, J. Am. Chem. Soc., 122, 907-921 (2000).

  35. J. Lee, J. Pillardy, C. Czaplewski, Y. Arnautova, D. R. Ripoll, A Liwo, K. D. Gibson, R. J. Wawak and H. A. Scheraga, Efficient parallel algorithms in global optimization of potential energy functions, Comp. Phys. Comm., 128, 399-411 (2000).

  36. C. Czaplewski, S. Rodziewicz-Motowidło, A. Liwo, D.R. Ripoll, R.J. Wawak, H.A. Scheraga, Molecular simulation study of cooperativity in hydrophobic association, Protein Sci., 9, 1235-1245 (2000).

  37. W.J. Wedemeyer, Y.A. Arnautova, J. Pillardy, R.J. Wawak, C. Czaplewski, H.A. Scheraga, Reply to ``Comment on 'Crystal structure prediction by global optimization as a tool for evaluating potentials: Role of the dipole moment correction term in successful predictions''' by B. P. van Eijck and J. Kroon, J. Phys. Chem. B, 33, 8090-8092 (2000).

  38. S. Rodziewicz-Motowidło, A. Legowska, X.F. Qi, C. Czaplewski, A. Liwo A, P. Sowinski, W. Mozga, J. Olczak, J. Zabrocki, K. Rolka, Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis, J. Pept. Res., 56, 132-146 (2000).

  39. M. Pasenkiewicz-Gierula, K. Murzyn, T. Rog, C. Czaplewski, Molecular dynamics simulation studies of lipid bilayer systems, Acta Biochim. Pol., 47, 601-611 (2000).

  40. M. Pasenkiewicz-Gierula, G. Jezierski, K. Murzyn, T. Rog, C. Czaplewski, J. Ciarkowski, Biofizyczne badania błon i białek metodą symulacji dynamiki molekularnej, Biotechnologia, 2, 83-97 (2000).

  41. A. Liwo, J. Pillardy, C. Czaplewski, J. Lee, D.R. Ripoll, M. Groth, S. Rodziewicz-Motowidło, R. Kazmierkiewicz, R.J. Wawak, S. Ołdziej, H.A. Scheraga, UNRES - a united-residue force field for energy-based prediction of protein structure - origin and significance of multibody terms, RECOMB 2000, Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, R. Shamir, S. Miyano, S. Istrail, P. Pevzner, M. Waterman (Eds.), April 8-11, Tokyo, Japan, published by ACM, New York, pp. 193-200.

  42. J. Pillardy, C. Czaplewski, W.J. Wedemeyer, H.A. Scheraga, Conformation-Family Monte Carlo (CFMC): An efficient computational method for identifying the low-energy states of a macromolecule, Helvetica Chimica Acta, 83, 2214-2230 (2000).

  43. P. Drabik, E. Politowska, C. Czaplewski, F. Kasprzykowski, L. Łankiewicz, J. Ciarkowski, Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases, Acta Biochim. Pol., 47, 1061-1066 (2000).

  44. I. Liepina, C. Czaplewski, P. Janmey, A. Liwo. Molecular dynamics of the gelsolin-derived peptide binding to a PIP2-containing lipid bilayer, Peptides 2000, Proceedings of the 26th Symposium of the European Peptide Society, Eds. J. Martinez and J.-A. Fehrentz (eds.), 987-988, (2001).

  45. J. Malicka, M. Groth, J. Karolczak, C. Czaplewski, A. Liwo, W. Wiczk, Influence of solvents and leucine configuration at position 5 on tryptophan fluorescence in cyclic enkephalin analogues, Biopolymers, 58, 447-457 (2001).

  46. J. Malicka, M. Groth, C. Czaplewski, J. Karolczak, A. Liwo, W. Wiczk, Influence of solvent and configuration of residues at positions 2 and 3 on distance and mobility of pharmacophore groups at positions 1 and 4 in cyclic enkephalin analogues, Biopolymers, 59, 180-190 (2001).

  47. J. Pillardy, C. Czaplewski, A. Liwo, J. Lee, D.R. Ripoll, R. Kaźmierkiewicz, S. Ołdziej, W.J. Wedemeyer, K.D. Gibson, Y.A. Arnautova,J. Saunders, Y-J. Ye, and H.A. Scheraga, Recent improvements in prediction of protein structure by global optimization of a potential energy function, Proc. Nat. Acad. Sci., 98, 2329-2333 (2001).

  48. J. Malicka J, R. Ganzynkowicz R, M. Groth, C. Czaplewski, J. Karolczak, A. Liwo A, W. Wiczk, Fluorescence decay time distribution analysis of cyclic enkephalin analogues; Influence of solvent and Leu configuration in position on conformation, Acta Biochim. Pol., 48, 95-102 (2001).

  49. A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga, Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field, J. Chem. Phys., 115, 2323-2347 (2001).

  50. J. Pillardy, C. Czaplewski, A. Liwo A, W.J. Wedemeyer, J. Lee, D.R. Ripoll, P. Arlukowicz, S. Ołdziej, Y.A. Arnautova, H.A. Scheraga Development of physics-based energy functions that predict medium-resolution structures for proteins of the alpha,beta and alpha/beta structural classes, J. Phys. Chem. B, 105, 7299-7311 (2001).

  51. J. Lee, D.R. Ripoll, C. Czaplewski, J. Pillardy, W.J. Wedemeyer WJ, H.A. Scheraga Optimization of parameters in macromolecular potential energy functions by conformational space annealing, J. Phys. Chem. B, 105, 7291-7298 (2001).

  52. M. Groth, J. Malicka, S. Rodziewicz-Motowidło S, C. Czaplewski C, L. Klaudel, W. Wiczk, A. Liwo Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: Application to the calibration of mean-field solvation models, Biopolymers, 60, 79-95 (2001).

  53. S. Rodziewicz-Motowidło, A. Lesner, A. Legowska, C. Czaplewski, A. Liwo, K. Rolka, R. Patacchini R, L. Quartara. Synthesis, activity on NK-(3) tachykinin receptor and conformational solution studies of scyliorhinin II analogs modified at position 16, J. Pept. Res., 58, 159-172 (2001).

  54. J. Pillardy, Y.A. Arnautova, C. Czaplewski K.D. Gibson, H.A. Scheraga, Conformation-family Monte Carlo: A new method for crystal structure prediction, Proc. Nat. Acad. Sci., 98, 12351-12356 (2001).

  55. P. Drabik, A. Liwo, C. Czaplewski, J. Ciarkowski, The investigation of the effects of counterions in protein dynamics simulations, Protein Eng., 14, 747-752 (2001).

  56. H.A. Scheraga, J. Pillardy, A. Liwo, J. Lee, C. Czaplewski, D.R. Ripoll, W.J. Wedemeyer, Y.A. Arnautova, Evolution of physics-based methodology for exploring the conformational energy landscape of proteins, J. Comput. Chem., 23, 28-34 (2002).

  57. B. Betlakowska, B. Banecki, C. Czaplewski, L, Łankiewicz and W. Wiczk, Reaction of 4-benzylidene-2-methyl-5-oxazolone with amines. Part II Influence of substitutents in para position in the phenyl ring and a substituent on amine nitrogen atom on the reraction kinetics, Int. J. Chem. Kinetics, 34, 148-155 (2002).

  58. C. Czaplewski, D.R. Ripoll, A. Liwo, S. Rodziewicz-Motowidło, R.J. Wawak, H.A. Scheraga, Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models? Int. J. Quant. Chem,88, 41-55 (2002).

  59. C. Czaplewski, S. Rodziewicz-Motowidło, A. Liwo, D.R. Ripoll, R.J. Wawak and H.A. Scheraga, Comment on "Anti-cooperativity in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond" [J. Chem. Phys. 115, 1414 (2001)], J. Chem. Phys.,116, 2665-2667 (2002).

  60. A. Liwo, P. Arłukowicz, C. Czaplewski, S. Ołdziej, J. Pillardy, H.A. Scheraga, A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field, Proc. Nat. Acad. Sci., 99, 1937-1942 (2002).

  61. J. Malicka, M. Groth, C. Czaplewski, W. Wiczk, A. Liwo, Conformational studies of cyclic enkephalin, analogues with L- or D-proline in position 3, Biopolymers, 63, 217-231 (2002).

  62. Y.A. Arnautova, J. Pillardy, C. Czaplewski, H.A.Scheraga, Global optimization-based method for deriving intermolecular potential parameters for crystals, J. Phys. Chem. B, 107, 712-723 (2002).

  63. C. Czaplewski, S. Rodziewicz-Motowidło, M. Dąbal, A. Liwo, D.R. Ripoll, H.A. Scheraga, Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles, Biophys. Chem., 105, 339-359 (2003); erratum Biophys. Chem., 111: 267-271 (2004).

  64. I. Liepina, C. Czaplewski, P. Janmey, A. Liwo, Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate, Biopolymers, 71, 49-70 (2003).

  65. I. Liepina, P. Janmey, C. Czaplewski, A. Liwo, Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain, J.Mol.Struct-Theochem, 630, 309-313 (2003).

  66. K. Maksimiak, S. Rodziewicz-Motowidło, C. Czaplewski, A. Liwo, and H.A. Scheraga, Molecular Simulation Study of the Potentials of Mean Force for the Interactions between Models of Like-Charged and between Charged and Nonpolar Amino Acid Side Chains in Water, J. Phys. Chem. B, 107, 13496-13504, (2003).

  67. I. Liepina, P. Janmey, C. Czaplewski, A. Liwo, Towards gelsolin amyloid formation, Biopolymers, 76, 543-548 (2004).

  68. C. Czaplewski, A. Liwo, J. Pillardy, S. Ołdziej, H.A. Scheraga, Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation, Polymer, 45, 677-686 (2004).

  69. C. Czaplewski, S. Ołdziej, A. Liwo and H.A. Scheraga, Prediction of the structures of proteins with the UNRES force field including dynamic formation and breaking of disulfide bonds, Protein Eng., Design &Selection, 17, 29-36 (2004).

  70. J. Malicka, C. Czaplewski, M. Groth, W. Wiczk, S. Ołdziej, L. Łankiewicz, J. Ciarkowski, A. Liwo, Use of NMR and fluorescence spectroscopy as well as theoretical conformational analysis in confomration-activity studies of cyclic enkephalin analogues, Current Topics in Medicinal Chemistry, 4, 123-133 (2004)

  71. H.A. Scheraga, A. Liwo, S. Oldziej, C. Czaplewski, J. Pillardy, D.R. Ripoll, J.A. Vila, R. Kazmierkiewicz, J.A. Saunders, Y.A. Arnautova, A. Jagielska, M. Chinchio, M. Nanias, The protein folding problem: Global optimization of force fields, Frontiers in Bioscience , 9, 3296-3323 Suppl. S (2004).

  72. A. Liwo, S. Oldziej, C. Czaplewski, U. Kozlowska, H.A. Scheraga, Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems, J. Phys. Chem. B, 108, 9421-9438, (2004).

  73. A. Liwo, P. Arlukowicz, S. Ołdziej, C. Czaplewski, M. Makowski, H.A. Scheraga, Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models, J. Phys. Chem. B. 108 16918-16933 (2004).

  74. S. Ołdziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga, Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins, J. Phys. Chem. B. 108 16934-16949 (2004).

  75. S. Ołdziej, J. Łagiewka, A. Liwo, C. Czaplewski, M. Chinchio, M. Nanias, H.A. Scheraga, Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization, J. Phys. Chem. B. 108 16950-16959 (2004).

  76. K. Lee, C. Czaplewski, S.Y. Kim, J. Lee An Efficient Molecular Docking Using Conformational Space Annealing, J. Comput. Chem., 26 78-87 (2005).

  77. W. Anusiewicz, J. Berdys-Kochańska, C. Czaplewski, M. Sobczyk, E.M. Daranowski, P. Skurski, J. Simons, Charge Loss in Gas-Phase Multiply Negatively Charged Oligionucleotides, J. Phys. Chem. A, 109 240-249 (2005).

  78. C. Czaplewski, A. Liwo, D.R. Ripoll and H.A. Scheraga, Molecular origin of anticooperativity in hydrophobic association, J. Phys. Chem. B, 109 8108-8119 (2005).

  79. S. Ołdziej, C. Czaplewski, A. Liwo, M. Chinchio, M. Nanias, J. A. Vila, M. Khalili, Y. A. Arnautova, A. Jagielska, M. Makowski, H. D. Schafroth, R. Kazmierkiewicz, D. R. Ripoll, J. Pillardy, J. A. Saunders, Y. K. Kang, K. D. Gibson, and H. A. Scheraga, Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests, Proc. Nat. Acad. Sci., 102, 7547-7552 (2005).

  80. M. Nanias, M. Chinchio, S. Ołdziej, C. Czaplewski, H.A. Scheraga, Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC, J. Comput. Chem., 26 1472-1486 (2005).

  81. C. Czaplewski, S. Kalinowski, A. Liwo, H.A. Scheraga, Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods, Mol. Phys., 103 3153-3167 (2005).

  82. C. Czaplewski, S. Kalinowski, A. Liwo, D.R. Ripoll, H.A. Scheraga, Reply to ``Comment on Molecular origin of anticooperativity in hydrophobic association'', J. Phys. Chem. B, 109 21222-21224 (2005).

  83. M. Nanias, C. Czaplewski, H.A. Scheraga, Replica exchange and multicanonical algorithms with the coarse-grained united-residue (UNRES) force field, J. Chem. Theory Comput., 2 513-528 (2006).

  84. I. Liepina, S. Ventura, C. Czaplewski, A. Liwo, Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides, J. Pept. Sci., 12, 780-789 (2006).

  85. M. Chinchio, C. Czaplewski, S. Oldziej, H.A. Scheraga, A hierarchical multiscale approach to protein structure prediction: Production of low-resolution packing arrangements of helices and refinement of the best models with a united-residue force field, Multiscale Mod. Sim., 5 1175-1195 (2006).

  86. H. Scheraga, A. Liwo, S. Ołdziej, C. Czaplewski, J. Pillardy, J. Lee, D.R. Ripoll, J.A. Vila, R. Kaźmierkiewicz, J.A. Saunders, Y.A. Arnautova, K.D. Gibson, A. Jagielska, M. Khalili, M. Chinchio, M. Nanias, Y.K. Kang, H. Schafroth, A. Ghosh, R. Elber and M. Makowski, The Protein Folding Problem, New Algorithms for Macromolecular Simulation, Series: Lecture Notes in Computational Science and Engineering, Vol. 49 B. Leimkuhler, C. Chipot, R. Elber, A. Laaksonen, A. Mark, T. Schlick, C. Schütte, R. Skeel (Eds.), 89-100 (2006)

  87. H.A. Scheraga, A. Liwo, S. Ołdziej, C. Czaplewski, M. Khalili, J.A. Villa, D.R. Ripoll, The Two Aspects of the Protein Folding Problem, NIC Series Volume 34: Proceedings of the NIC Workshop: From Computational Biophysics to Systems Biology 2006 U.H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.),37-44 , 2006

  88. C. Czaplewski, S. Kalinowski, S. Ołdziej, A. Liwo, H. A. Scheraga, Multiplexed-Replica Exchange Molecular Dynamics with the UNRES Force-Field as an Effective Method for Exploring the Conformational Energy Landscape of Proteins. NIC Series Volume 34: Proceedings of the NIC Workshop: From Computational Biophysics to Systems Biology 2006 U.H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), 63-66, 2006

  89. I. Liepina, S. Ventura, C. Czaplewski, A. Liwo, Molecular Dynamics Study of Amyloid Formation of Two Abl-SH3 Domain Peptides NIC Series Volume 34: Proceedings of the NIC Workshop: From Computational Biophysics to Systems Biology 2006 U.H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), 103-106, 2006

  90. A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Ołdziej, H. A. Scheraga, Optimization of the United-Residue UNRES Force Field for Langevin Dynamics Simulations NIC Series Volume 34: Proceedings of the NIC Workshop: From Computational Biophysics to Systems Biology 2006 U.H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.),107-110 , 2006

  91. I. Liepina, S. Ventura, C. Czaplewski, A. Liwo. Molecular dynamics study of two ABL-SH3 domain peptides towards amyloid formation Peptides 2006, Proceedings of the 29th European Peptide Symposium, K. Rolka, P. Rekowski, J. Silberring (Eds.), 782-783, (2007)

  92. R. Wyrzykowski, N. Meyer, T. Olas, L. Kuczynski, B. Ludwiczak, C. Czaplewski and S. Ołdziej, Meta-computations on the CLUSTERIX Grid, Applied Parallel Computing, State of the Art in Scientific Computing, Series: Lecture Notes in Computer Science, Volume 4699, B. Kågström, E. Elmroth, J. Dongarra, J. Waśniewski (Eds.), 489-500, (2007)

  93. A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Ołdziej, K. Wachucik, H.A. Scheraga, Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins, J. Phys. Chem. B, 111 260-285 (2007).

  94. M. Makowski, E. Sobolewski, C. Czaplewski, A. Liwo, S. Ołdziej, J.H. No, H.A. Scheraga, Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains, J. Phys. Chem. B, 111 2925-2931 (2007).

  95. M. Witt, J. Ciarkowski, C. Czaplewski, Molecular simulations of rhodopsin tetrameter, Prot. Pept. Lett., 14 381-387 (2007).

  96. M. Chinchio, C. Czaplewski, A. Liwo, S. Ołdziej, H. A. Scheraga, Dynamic formation and breaking of disulfide bonds in molecular dynamics simulations with the UNRES force field, J. Chem. Theor. Comput, 3 1236-1248 (2007).

  97. E. Sobolewski, M. Makowski, C. Czaplewski, A. Liwo, S. Ołdziej, H.A. Scheraga, Potential of mean force of hydrophobic association: Dependence on solute size, J. Phys. Chem. B, 111 10765-10774 (2007).

  98. A. Liwo, C. Czaplewski, S. Ołdziej, M. Chinchio, A. V. Rojas, M. Khalili, M. Makowski, S. Kalinowski, U. Kozłowska, R. K. Murarka, H. A. Scheraga, Mesoscopic Dynamics with the UNRES Force Field - a Tool for Studying the Kinetics and Thermodynamics of Protein Folding NIC Series Volume 36: Proceedings of the NIC Workshop: From Computational Biophysics to Systems Biology 2007 U.H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), 31-36, 2007

  99. H. A. Scheraga, A. Liwo, C. Czaplewski, S. Ołdziej, Evolution of Experimental and Theoretical Determinations of Protein Structure and Protein Folding Pathways, NIC Series Volume 36: Proceedings of the NIC Workshop: From Computational Biophysics to Systems Biology 2007 U.H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), 45-54, 2007

  100. I. Liepina, S. Ventura, C. Czaplewski, A. Liwo, Multiple Beta-Sheet Molecular Dynamics of Two Abl-SH3 Domain Peptides, NIC Series Volume 36: Proceedings of the NIC Workshop: From Computational Biophysics to Systems Biology 2007 U.H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), 215-218, 2007

  101. A. Liwo, C. Czaplewski, S. Ołdziej, U. Kozłowska, M. Makowski, S. Kalinowski, R. Kaźmierkiewicz, H. Shen, G. Maisuradze, H. A. Scheraga, Optimization of a Physics-Based United-Residue Force Field (UNRES) for Protein Folding Simulations NIC Series Volume 39:Proceedings of the NIC Symposium 2008, G. Münster, D. Wolf, M. Kremer (Eds.), 63-70, 2008

  102. S. Rodziewicz-Motowidło, E. Sikorska, M. Oleszczuk, C. Czaplewski, Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part II: studies in the SDS micelle, J. Pept. Sci., 14 85-96 (2008).

  103. A. Liwo, C. Czaplewski, S. Ołdziej, H. A. Scheraga, Computational techniques for efficient conformational sampling of proteins, Curr. Opinion Struct. Biol., 18 134-139 (2008).

  104. D.S. Kleinerman, C. Czaplewski, A. Liwo, H. A. Scheraga, Implementations of Nose-Hoover and Nose-Poincare thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain, J. Chem. Phys., 128 245103 (2008).

  105. H. Shen, C. Czaplewski, A. Liwo, H.A. Scheraga, Implementation of a Serial Replica Exchange Method in a physics-based united-residue (UNRES) force field, J. Chem. Theor. Comput, 4 1386-1400 (2008).

  106. S. Rodziewicz-Motowidło, C. Czaplewski, S. Łuczak, J. Ciarkowski, Conformation-activity relationships of cyclo-constrained mu/delta opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin, J. Pept. Sci., 14 898-902 (2008).

  107. A. Zieleniak, S. Rodziewicz-Motowidło, L. Rusak, N.N. Chung, C. Czaplewski, E. Witkowska, P.W. Schiller, J. Ciarkowski, J. Izdebski, Deltorphin analogs restricted via a urea bridge: structure and opioid activity, J. Pept. Sci., 14 830-837 (2008).

  108. M. Makowski, E. Sobolewski, C. Czaplewski, S. Ołdziej, A. Liwo, H.A. Scheraga, Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains J. Phys. Chem. B, 112 11385-11395 (2008).

  109. C. Czaplewski, P. Czaplewska, J. Romankiewicz, W. Wiczk, The binding of peptides containing tyrosine residue to β-cyclodextrin, Peptides 2008, Proceedings of the 30th European Peptide Symposium, Hikka Lankinen (Ed.), 572-573, (2008).

  110. S. Łuczak, J. Ciarkowski, S. Rodziewicz-Motowidło, C. Czaplewski, J. Wójcik, M. Nowakowski, M. Kwasiborska, M. Małgorzata, J. Izdebski, M. Oleszczuk, P.W. Schiller, N.N. Chung, Cyclic enkephalin analogs containing two alkylurea units, Peptides 2008, Proceedings of the 30th European Peptide Symposium, Hikka Lankinen (Ed.), 302-303, (2008).

  111. I. Liepina, C. Czaplewski, A. Liwo, K. Pajuste, V. Ose, G. Duburs, 1,4-DHP-lipid forms rod like micellae, Peptides 2008, Proceedings of the 30th European Peptide Symposium, Hikka Lankinen (Ed.), 632-633, (2008).

  112. A. Liwo, C. Czaplewski, S. Ołdziej, A.V. Rojas, R. Kaźmierkiewicz, M. Makowski, R.K. Murarka and H.A. Scheraga, Chapter 8. Simulation of protein structure and dynamics with the coarse-grained UNRES force field, in Coarse-Graining of Condensed Phase and Biomolecular Systems, edited by G.A. Voth, CRC Press Taylor and Francis Group, pp. 107-122 (2008). ISBN 978-1420059557

  113. I. Liepina, S. Ventura, C. Czaplewski, A. Liwo, Dynamics study on single and multiple beta-sheets, in Advances in Experimental Medicine and Biology, 611, S. DelValle, E. Escher, W.D. Lubell, Editors, The Proceedings of the 20th American Peptide Symposium, Montreal, June 26-30 2007, pp. 293-294 (2009).

  114. J. Ciarkowski, A. Zieleniak, S. Rodziewicz-Motowidło, Ł. Rusak, N.N. Chung, C. Czaplewski, E. Witkowska, P.W. Schiller and J. Izdebski, Deltorphin analogs restricted via a urea bridge: structure and opioid activity, in Advances in Experimental Medicine and Biology, 611, S. DelValle, E. Escher, W.D. Lubell, Editors, The Proceedings of the 20th American Peptide Symposium, Montreal, June 26-30 2007, pp. 491-492 (2009).

  115. J. Ciarkowski, C. Czaplewski, S. Łuczak, S. Rodziewicz-Motowidło and P.W. Schiller, Conformation-activity relationships of cyclo-constrained / opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin, in Advances in Experimental Medicine and Biology, 611, S. DelValle, E. Escher, W.D. Lubell, Editors, The Proceedings of the 20th American Peptide Symposium, Montreal, June 26-30 2007, pp. 489-490 (2009).

  116. C. Czaplewski, S. Kalinowski, A. Liwo, and H.A. Scheraga, Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with β and α+β Proteins, J. Chem. Theory Comput., 5 627-640 (2009).

  117. E. Sobolewski, M. Makowski, S. Ołdziej, C. Czaplewski, A. Liwo, H.A. Scheraga, Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I. Molecular dynamics study of a pair of methane molecules in water at various temperatures, Protein Eng., Design & Selection, 22 547-552 (2009).

  118. K. Guzow, M. Milewska, C. Czaplewski, W. Wiczk, A DFT/TDDFT study of the structure and spectroscopic properties of 5-methyl-2-(8-quinolinyl)benzoxazole and its complexes with Zn(II) ion, Spectrochim. Acta A, 75 773-781 (2010).

  119. M. Makowski, C. Czaplewski, A. Liwo, H.A. Scheraga, Potential of mean force of association of large hydrophobic particles: towards the nanoscale limit, J. Phys. Chem. B, 114 993-1003 (2010).

  120. A. Liwo, S. Ołdziej, C. Czaplewski, D. Kleinerman, P. Blood and H.A. Scheraga, Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics, J. Chem. Theory Comput., 6 890-909 (2010).

  121. K. Smalara, A. Giełdon, M. Bobrowski, J. Rybicki, C. Czaplewski, Theoretical study of polymerization mechanism of p-xylylene based polymers, J. Phys. Chem. A, 114 4296-4303 (2010).

  122. G. Maisuradze, P. Senet, C. Czaplewski, A. Liwo, H.A. Scheraga Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field, J. Phys. Chem. A, 114 4471-4485 (2010). [feature article]

  123. D. Jagieła, C. Czaplewski, A. Liwo, S. Ołdziej, H.A. Scheraga, Global parameter optimization of a physics-based united residue force field (UNRES) for proteins, inSiDE, Vol. 8 No. 1, eds. H-G. Hegering, T. Lippert, M. Resch, Gauss Centre for Supercomputing, 40-45 (2010).

  124. C. Czaplewski, A. Liwo, M. Makowski, H.A. Scheraga, Hydrophobic Interactions and Protein Folding, in Molecular Liquids Review Book, volume ``Thermodynamics of Amino Acid and Protein Solutions'', edited by J. Tsurko and W. Kunz, Transworld Research Network, pp. 1-18 (2010). ISBN 978-81-7895-473-8

  125. S. Ołdziej, C. Czaplewski, A. Liwo, H.A. Scheraga, Towards temperature dependent coarse-grained potential of side-chain interactions for protein folding simulations, BIBE, pp.263-266, IEEE International Conference on Bioinformatics and Bioengineering, Philadelphia, Pennsylvania USA, May 31-June 03 (2010).

  126. A. Legowska, D. Debowski, R. Lukajtis, M. Wysocka, C. Czaplewski, A. Lesner, K. Rolka, Implication of the disulfide bridge in trypsin inhibitor SFTI-1 in its interaction with serine proteinases, Bioorg. Med. Chem., 18 8188-8193 (2010).

  127. V. Duka, I. Bestel, C. Czaplewski, A. Liwo, I. Liepina Molecular modeling of single and multiple beta-sheets of Amyloid beta protein 25-35 Peptides 2010, Proceedings of the 31th European Peptide Symposium, M. Lebl, M. Meldal, K.J. Jensen, T. Hoeg-Jensen (Eds.), 572-573, (2010).

  128. D. Lapidus, S. Ventura, C. Czaplewski, A. Liwo, I. Liepina Molecular dynamics of amylin amyloid single and multiple beta sheets Peptides 2010, Proceedings of the 31th European Peptide Symposium, M. Lebl, M. Meldal, K.J. Jensen, T. Hoeg-Jensen (Eds.), 570-571, (2010).

  129. I. Liepina, A. Zemitis, G. Duburs, C. Czaplewski, A. Liwo, Tubomicelle of gene transfection agent 1,4-dihydropyridine lipid and its binding with DNA Peptides 2010, Proceedings of the 31th European Peptide Symposium, M. Lebl, M. Meldal, K.J. Jensen, T. Hoeg-Jensen (Eds.), 630-631, (2010).

  130. C. Czaplewski, A. Liwo, M. Makowski, S. Ołdziej, H.A. Scheraga, Coarse-Grained Models of Proteins: Theory and Applications, chapter 3 in Multiscale approaches to protein modeling, edited by A. Koliński, Springer, pp 35-84 (2011). ISBN 978-1-4419-6888-3

  131. A. Giełdoń, C. Czaplewski, K. Smalara, M. Bobrowski, Molecular dynamics simulation of the growth of poly(chloro-para-xylylene) films, J. Mol. Mod., 17 2725-2733 (2011).

  132. I. Liepina, C. Czaplewski, A. Liwo, G. Duburs, 1,4-DHP-lipid parameters and rod like micellae, J. Biophys. Chem., 2 386-394 (2011).

  133. E. Gołaś, G. Maisuradze, P. Senet, S. Ołdziej, C. Czaplewski, H.A. Scheraga, A. Liwo, Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics, J. Chem. Theory Comput., 8 1750-1764 (2012).

  134. S. Ołdziej, C. Czaplewski, A. Liwo, J.A. Vila, H.A. Scheraga, Computing of structure, dynamics, and thermodynamics of proteins, in E.H. Egelman, editor: Comprehensive Biophysics, Vol 1, Biophysical Techniques for the Structural Characterization of Macromolecules, edited by H. J. Dyson. Oxford: Academic Press (2012) pp. 494-513. ISBN 978-0123749208

  135. C. Czaplewski, A. Giełdoń, K. Smalara, M. Bobrowski, Molecular Dynamics Simulation of Polymerization of p-Xylylene, AIP Conf. Proc. 1504, 1142 (2012) COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING: Advances in Computational Science: Lectures presented at the International Conference on Computational Methods in Sciences and Engineering 2009 (ICCMSE 2009), Rhodes, Greece , 29 Sep - 4 Oct 2009.

  136. D. Lapidus, V. Duka, V. Stonkus, C. Czaplewski, A. Liwo, S. Ventura, I. Liepina, Multiple β-sheet molecular dynamics of amyloid formation from two Abl-SH3 domain peptides, Biopolymers (Pept. Sci.), 98 557-566 (2012).

  137. K. Guzow, M. Czerwińska, A. Ceszlak, M. Kozarzewska, M. Szabelski, C. Czaplewski, A. Łukaszewicz, A.A.Kubicki, W. Wiczk, Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives – experimental and theoretical studies, Photochem. Photobiol. Sci., 12, 284-297 (2013).

  138. A. Lewandowska, K. Guzow, D. Wróblewski, C. Czaplewski, W. Wiczk, Acid-base properties of 3-[2-(pyridyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies. J. Photochem. Photobiol. A - Chemistry, 258, 10-16 (2013).

  139. P. Krupa, A. Sieradzan, S. Rackovsky, M. Baranowski, S. Ołdziej, H.A. Scheraga, A. Liwo, C. Czaplewski, Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states. J. Chem. Theory Comput., 9, 4620-4632 (2013).

  140. Y. He, M. Mozolewska, P. Krupa, A.K. Sieradzan, T. Wirecki, A. Liwo, K. Kalichvili, S. Rackovsky, D. Jagieła, R. Ślusarz, C. Czaplewski, S. Ołdziej, H.A. Scheraga, Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Proc. Nat. Acad. Sci., 110, 14936-14941 (2013).

  141. E.I. Gołaś, C. Czaplewski, Computational Simulation and Analysis of a Candidate for the Design of a Novel Silk-based Biopolymer. Biopolymers, 101, 915-923 (2014).

  142. A. Liwo, M. Baranowski, C. Czaplewski, E. Gołaś. Y He, D. Jagieła, P. Krupa, M. Maciejczyk, M. Makowski, M.A. Mozolewska, A. Niadzvedtski, S. Oldziej, H.A. Scheraga, A.K. Sieradzan, R. Ślusarz, T. Wirecki, Y. Yin, B. Zaborowski, A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. J. Mol. Model., 20 2306 (2014)

  143. I. Bylińska, M. Wierzbicka, C. Czaplewski and W. Wiczk, Solvatochromic studies of pull-push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit. RSC Adv., 4, 48783-48795 (2014).

  144. R. Zhou, G.G. Maisuradze, D. SuXol,T. Todorovski,M.J. Macias, Y. Xiao, H.A. Scheraga, C. Czaplewski, A. Liwo, Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements. Proc. Nat. Acad. Sci., 111, 18243-18248 (2014).

  145. P. Krupa, M.A. Mozolewska, B. Rasulev, C. Czaplewski, J. Leszczynski. Towards mechanisms of nanotoxicity - interaction of gold nanoparticles with proteins and DNA. TASK Quarterly, 18, 337-341 (2014).

  146. E.I. Gołaś, C. Czaplewski, H.A. Scheraga, A. Liwo. Common functionally-important motions of the nucleotidebinding domain of Hsp70. Proteins, 83, 282-299 (2015).

  147. P. Krupa, M.A. Mozolewska, K. Joo, J. Lee, C. Czaplewski, A. Liwo. Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field. J. Chem. Inf. Model., 55, 1271-1281 (2015).

  148. A.K. Sieradzan, P. Krupa, H.A. Scheraga, A. Liwo, C. Czaplewski. Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations. J. Chem. Theory Comput., 11 817–831 (2015).

  149. B. Zaborowski, D. Jagieła, C. Czaplewski, A. Hałabis, A. Lewandowska, W. Żmudzińska, S. Ołdziej, A. Karczyńska, C. Omieczynski, T. Wirecki, A. Liwo. A maximum-likelihood approach to force-field calibration. J. Chem. Inf. Model., 55, 2050-2070 (2015).

  150. M. Wierzbicka, I. Bylińska, C. Czaplewski and W. Wiczk, Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives. RSC Adv., 5, 29294-29303 (2015).

  151. M. Wierzbicka, I. Bylińska, A. Sikorski, C. Czaplewski and W. Wiczk, Experimental and theoretical studies of spectroscopic properties of simple symmetrically substituted diphenylbuta-1,3-diyne derivatives. Photochem. Photobiol. Sci., 14, 2251-2260 (2015).

  152. I. Bylińska, M. Wierzbicka, C. Czaplewski and W. Wiczk, Photophysical properties of symmetrically substituted diarylacetylenes and diarylbuta-1,3-diynes. Photochem. Photobiol. Sci., 15, 45-56 (2016).

  153. 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, Temperature-dependent structure-property modeling of viscosity for ionic liquids. Fluid Phase Equilibria, 427, 9-17 (2016).

  154. N. Gruba, M. Wysocka, M. Brzezińska, D. Dębowski, M.Sieńczyk, E. Gorodkiewicz, T. Guszcz, C. Czaplewski, K. Rolka and A. Lesner, Bladder cancer detection using a peptide substrate of the 20S proteasome. FEBS J., 283, 2929–2948 (2016).

  155. P. Krupa, M.A. Mozolewska, M. Wiśniewska, Y. Yin, Y. He, A.K. Sieradzan, R. Ganzynkowicz, A.G. Lipska, A. Karczyńska1, M. Ślusarz, R. Ślusarz, A. Giełdoń, C. Czaplewski, D. Jagieła, B. Zaborowski, H.A. Scheraga, A. Liwo, Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinformatics, 32, 3270–3278 (2016).

  156. M. Mozolewska, P. Krupa, B. Zaborowski, A. Liwo, J. Lee, K. Joo, C. Czaplewski, Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. J. Chem. Inf. Model., 56, 2263-2279 (2016).

  157. A. Liwo, C. Czaplewski, S. Ołdziej, B. Zaborowski, D. Jagieła, J. Lee, Chemoinformatics methods for studying biomolecules, in Handbook of computational chemistry, edited by J. Leszczyński. Springer (2017) pp. 2183-2199. ISBN 978-3-319-27281-8

  158. M.A. Mozolewska, A.K. Sieradzan, A. Niadzvedstki, C. Czaplewski, A. Liwo, P. Krupa, Role of the sulfur to α-carbon thioether bridges in thurincin H, J. Biomol. Struct. Dyn., 35, 2868-2879 (2017).

  159. A. Giełdoń, M. Bobrowski, A. Bielicka-Giełdoń, C. Czaplewski, Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids, J.Mol.Liq. 225, 467–474 (2017).

  160. C. Czaplewski, K. Smalara; A. Giełdoń, M. Bobrowski, Polymerization of chloro-p-xylylenes, quantum-chemical study, J.Mol.Model. 23, 40 (2017).

  161. M. Szyszkowska, C. Czaplewski, W. Wiczk, Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation, J. Mol. Structure 1138, 81-89 (2017).

  162. A. Karczyńska, C. Czaplewski, P. Krupa, M. Mozolewska, K. Joo, J. Lee, A. Liwo, Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins, J. Comput. Chem. 38, 2730–2746 (2017).

  163. 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. O"ldziej, T. Wirecki, Y. Yin, B. Zaborowski, H.A. Scheraga, Microscopic Physics-Based Models of Proteins and Nucleic Acids: UNRES and NARES, 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

  164. A. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, A. Liwo, C. Czaplewski, Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information, Proteins: Struct. Funct. Bioinf., 86, 228-239 (2018). CASP12 special issue.

  165. A. Lewandowska, D. Wroblewski, K. Guzow, M. Milewska, C. Czaplewski, W. Wiczk, Acid-base properties of 3-[2-(n-quinolinyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies. J. Photochem. Photobiol. A - Chemistry, 353, 191–199 (2018).

  166. E.I. Golas, M.A. Mozolewska, P. Krupa, C. Czaplewski, H.A. Scheraga, A. Liwo, Use of Coarse-Grained and All-Atom Molecular Dynamics to Study Hsp70 and Hsp40 Chaperone Action, in Frontiers in Structural Biology Vol. 1 edited by M.D. Galigniana, Bentham Publishers, pp 23-46 (2018). ISBN: 978-1-68108-616-3

  167. E. Lubecka, A. Sieradzan, C. Czaplewski, P. Krupa, A. Liwo, High performance computing with coarse-grained model of biological macromolecules. Supercomputing Frontiers and Innovations 5, 63-75 (2018).

  168. M. J. Grzeszczuk, A. Bak, A. M. Banas, P. Urbanowicz, S. Dunin-Horkawicz, A. Gieldon, C. Czaplewski, A. Liwo, E.K. Jagusztyn-Krynicka, 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. Plos One 13, e0195358 (2018).

  169. 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 Res. 46, W304-W309 (2018).

  170. 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, Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: test with CASP12 targets. J. Mol. Graph. Model. 83, 92-99 (2018).

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