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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Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubilityKuriata, A. et al.Nucleic Acids Research 47, W300-W307, 2019.
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structuresKuriata, A. et al.Nucleic Acids Research, gky356 , 2018.
Aggrescan3D standalone package for structure-based prediction of protein aggregation propertiesKuriata, A., Iglesias, V., Kurcinski, M., Ventura, S. & Kmiecik, S.Bioinformatics btz143, , 2019.
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding siteKurcinski, M., Jamroz, M., Blaszczyk, M., Koliński, A. & Kmiecik, S.Nucleic Acids Research 43 (W1), W419-W424, 2015.
A protocol for CABS-dock protein–peptide docking driven by side-chain contact informationKurcinski, M., Blaszczyk, M., Ciemny, M., Koliński, A. & Kmiecik, S.BioMedical Engineering OnLine, 16:73 , 2017.
Multiscale protein and peptide dockingKurcinski, M., Jamroz, M. & Koliński, A.Multiscale Approaches to Protein Modeling 21-34, 2011.
Flexible docking of peptides to proteins using CABS-dockKurcinski, M., Badaczewska-Dawid, A.E., Kolinski, M., Koliński, A. & Kmiecik, S.Protein Science, 29:211-222 , 2020.
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.
Hierarchical modeling of protein interactionsKurcinski, M. & Koliński, A.Journal of Molecular Modeling 13, 691–698, 2007.
CABS-flex standalone: a simulation environment for fast modeling of protein flexibilityKurcinski, M. et al.Bioinformatics bty685, 2018.
Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequencesKurcinski, M. & Koliński, A.The Journal of Steroid Biochemistry and Molecular Biology 103, 357–60, 2007.
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acidKurcinski, M. & Koliński, A.The Journal of Steroid Biochemistry and Molecular Biology 121, 124–9, 2010.
Flexible protein-peptide docking using CABS-dock with knowledge about the binding siteKurcinski, M., Ciemny, M., Blaszczyk, M., Koliński, A. & Kmiecik, S.Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 195-201, arXiv:1605.09269 , 2016.
Molar Excess Enthalpies and Volumes of Mixtures of 2,4,6-trimethylopyridyne with some Aliphatic AlcoholsKowalski, B., Kasprzycka-Guttman, T. & Koliński, A.Polish Journal of Chemistry 54, 1995, 1980.
Explicit-Solvent All-Atom Molecular Dynamics of Peptide AggregationKouza, M., Koliński, A., Buhimschi, I. & Kloczkowski, A.Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 541–558, 2019.
A numerical investigation into possible mechanisms by that the A629P mutant of ATP7A causes Menkes DiseaseKouza, M., Gowtham, S., Seel, M. & Hansmann, U.H.E.Phys Chem Chem Phys 12, 11390-7, 2010.
The GOR Method of Protein Secondary Structure Prediction, and its Application as Protein Aggregation Prediction ToolKouza, M., Faraggi, E., Koliński, A. & Kloczkowski, A.Methods in Molecular Biology 1484, 7-24, 2017.
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological ComplexesKouza, M., Banerji, A., Koliński, A., Buhimschi, I. & Kloczkowski, A.Molecules 23(8), 1995, 2018.
Velocity scaling for optimizing replica exchange molecular dynamicsKouza, M. & Hansmann, U.H.E.The Journal of Chemical Physics 134, 044124, 2011.
Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible modelKouza, M., Banerji, A., Koliński, A., Buhimschi, I.A. & Kloczkowski, A.Physical Chemistry Chemical Physics 19, 2990-9, 2017.
Folding of the protein domain hbSBDKouza, M. et al.Biophys J 89, 3353-61, 2005.
Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational studyKouza, M. et al.The Journal of Chemical Physics 148, 215106, 2018.
Folding Simulations of the A and B Domains of Protein GKouza, M. & Hansmann, U.H.E.The Journal of Physical Chemistry B 116, 6645-6653, 2012.
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.
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.

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