Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Biomolecules — dynamics & interactions

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2019
Protein Structure Prediction Using Coarse-Grained ModelsBlaszczyk, M. et al.Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 27–59, 2019.
2018
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structuresKuriata, A. et al.Nucleic Acids Research, gky356 , 2018.
Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold AssemblyDawid, A., Gront, D. & Koliński, A.Journal of Chemical Theory and Computation 14 (4), 2277–2287, 2018.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityGil-Garcia, M. et al.Molecular Pharmaceutics 15, 3846-3859, 2018.
In silico analysis of cytochrome P450 monooxygenases in chronic granulomatous infectious fungus Sporothrix schenckii: Special focus on CYP51.Matowane, R.Godfrey et al.Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1866(1), 166-177, 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
Biofunctionalisation of p-doped silicon with cytochrome c553 minimises charge recombination and enhances photovoltaic performance of the all-solid-state photosystem I-based biophotoelectrodeOlmos, J.David Jann et al.RSC Advances 7, 47854-47866, 2017.
Biofunctionalisation of p-doped silicon with cytochrome c553 minimises charge recombination and enhances photovoltaic performance of the all-solid-state photosystem I-based biophotoelectrodeOlmos, J.David Jann et al.RSC Advances 7, 47854-47866, 2017.
SURPASS Low-Resolution Coarse-Grained Protein ModelingDawid, A., Gront, D. & Koliński, A.Journal of Chemical Theory and Computation 13(11), 5766-5779, 2017.
Switch from thermal to force-driven pathways of protein refoldingKouza, M., Lan, P.Dang, Gabovich, A.M., Koliński, A. & Li, M.SuanThe Journal of Chemical Physics 146, 135101, 2017.
2016
Coarse-Grained Protein Models and Their ApplicationsKmiecik, S. et al.Chemical Reviews 116, 7898–7936, 2016.
2015
Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima.Wieteska, L. et al.Journal of Biotechnology 199, 69-76, 2015.
2014
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.Gniewek, P., Koliński, A., Kloczkowski, A. & Gront, D.BMC Bioinformatics 15, 22, 2014.
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.Gniewek, P., Koliński, A., Kloczkowski, A. & Gront, D.BMC Bioinformatics 15, 22, 2014.
Coarse-Grained Protein Models in Structure PredictionBlaszczyk, M. et al.Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed. 1, 25-53, 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.
2013
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular DynamicsWabik, J., Kmiecik, S., Gront, D., Kouza, M. & Koliński, A.International Journal of Molecular Sciences 14, 9893–9905, 2013.
2012
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profilesGront, D., Blaszczyk, M., Wojciechowski, P. & Koliński, A.Nucleic Acids Research 40, W257–62, 2012.
Chameleonicity and folding of the C-fragment of TOP7Gaye, M.L., Hardwick, C., Kouza, M. & Hansmann, U.H.E.EPL (Europhysics Letters) 97, 68003, 2012.
Coarse-grained modeling of mucus barrier propertiesGniewek, P. & Koliński, A.Biophysical Journal 102, 195–200, 2012.
Elastic network normal modes provide a basis for protein structure refinementGniewek, P., Koliński, A., Jernigan, R.L. & Kloczkowski, A.The Journal of Chemical Physics 136, 195101, 2012.
From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein AKmiecik, S., Gront, D., Kouza, M. & Koliński, A.The Journal of Physical Chemistry B 116, 7026–32, 2012.
How noise in force fields can affect the structural refinement of protein models?Gniewek, P., Koliński, A., Jernigan, R.L. & Kloczkowski, A.Proteins 80, 335–341, 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.
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.

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