Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Modeling Software & Servers

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Biomolecules — dynamics & interactions

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Publications

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2021
Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained DockingZalewski, M., Kmiecik, S. & Kolinski, M.Molecules 26(11), , 2021.
2019
Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force FieldsCiemny, M., Badaczewska-Dawid, A.E., Pikuzinska, M., Koliński, A. & Kmiecik, S.International Journal of Molecular Sciences 20, , 2019.
2018
Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network ModelsKmiecik, S., Kouza, M., Dawid, A., Kloczkowski, A. & Koliński, A.International Journal of Molecular Sciences 19, , 2018.
Mutation goals in the vitamin D receptor predicted by computational methods.Sicinska, W., Gront, D. & Sicinski, K.The Journal of Steroid Biochemistry and Molecular Biology 183, 210-220, 2018.
2017
Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motifCiemny, M., Kurcinski, M., Blaszczyk, M., Koliński, A. & Kmiecik, S.BioMedical Engineering OnLine, 16:71 , 2017.
2016
Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible dockingBlaszczyk, M. et al.Methods 93, 72–83, 2016.
2014
Mechanical unfolding of DDFLN4 studied by the coarse-grained knowledge-based CABS modelKouza, M., Jamroz, M., Gront, D., Kmiecik, S. & Koliński, A.TASK Quarterly 18, 373–378, 2014.
Mechanism of Folding and Binding of an Intrinsically Disordered Protein as Revealed by Ab Initio SimulationsKurcinski, M., Koliński, A. & Kmiecik, S.Journal of Chemical Theory and Computation 10, 2224–2231, 2014.
2012
Modeling Protein Structures and their Complexes with Sparse Experimental DataGront, D., Blaszczyk, M., Wabik, J. & Koliński, A.From Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 49–52, 2012.
Modelowanie Molekularne Białek Błonowych (Molecular Modeling of Membrane Proteins)Dawid, A., Kolinski, M., Koliński, A. & Kmiecik, S.Na pograniczu chemii i biologii (At the Treshold of Chemistry and Biology) vol. XXVIII, H. Koroniak, J. Barciszewski eds, Wydawnictwo Naukowe UAM, Poznań 223-238, 2012.
Multiscale Approach to Thermodynamics and Dynamics of a beta-Hairpin FoldingWabik, J., Gront, D., Kmiecik, S. & Koliński, A.From Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 213–216, 2012.
2011
Multibody coarse-grained potentials for native structure recognition and quality assessment of protein modelsGniewek, P., Leelananda, S.P., Koliński, A., Jernigan, R.L. & Kloczkowski, A.Proteins 79, 1923–9, 2011.
Multiscale approach to protein folding dynamicsKmiecik, S., Jamroz, M., Koliński, A. & Koliński, A.Multiscale Approaches to Protein Modeling 281-294, 2011.
Multiscale protein and peptide dockingKurcinski, M., Jamroz, M. & Koliński, A.Multiscale Approaches to Protein Modeling 21-34, 2011.
2010
Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulationsArad-Haase, G. et al.Biophys J 99, 238-47, 2010.
Modeling of loops in proteins: a multi-method approachJamroz, M. & Koliński, A.BMC Structural Biology 10, 5, 2010.
MSITE: a new computational tool for comparison of homological proteins in holo formSicinska, W. & Kurcinski, M.The Journal of Steroid Biochemistry and Molecular Biology 121, 34-42, 2010.
2009
Mechanical strength of 17,134 model proteins and cysteine slipknots.Sikora, M., Sulkowska, J.I. & Cieplak, M.PLoS Comput Biol 5, e1000547, 2009.
2007
Mechanical stretching of proteins—a theoretical survey of the Protein Data BankSulkowska, J.I. & Cieplak, M.Journal of Physics: Condensed Matter 19, , 2007.
2006
Modeling protein structure, dynamics and thermodynamics with reduced representation of conformational spaceKoliński, A. et al.NIC Workshop 2006: From Computational Biophysics to System Biology 34, 21-28, 2006.
2005
A minimal proteinlike lattice model: an alpha-helix motifPokarowski, P., Droste, K. & Koliński, A.The Journal of Chemical Physics 122, 214915, 2005.
2004
Model of three-dimensional structure of VDR bound with Vitamin D3 analogs substituted at carbon-2Sicinska, W., Rotkiewicz, P. & DeLuca, H.F.The Journal of Steroid Biochemistry and Molecular Biology 89-90, 107-10, 2004.
2003
A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native statePokarowski, P., Koliński, A. & Skolnick, J.Biophysical Journal 84, 1518–26, 2003.
2001
Model of three-dimensional structure of vitamin D receptor and its binding mechanism with 1alpha,25-dihydroxyvitamin D(3)Rotkiewicz, P., Sicinska, W., Koliński, A. & DeLuca, H.F.Proteins 44, 188–199, 2001.
2000
Monte Carlo simulation of designed helical proteinsSikorski, A., Koliński, A. & Skolnick, J.Acta Poloniae Pharmaceutica – Drug Research 57 Suppl, 119-21, 2000.

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