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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2021
Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained DockingZalewski, M., Kmiecik, S. & Kolinski, M.Molecules 26(11), , 2021.
Protein-protein docking with large-scale backbone flexibility using coarse-grained Monte-Carlo simulationsKurcinski, M., Kmiecik, S., Zalewski, M. & Koliński, A.International Journal of Molecular Sciences 22(14), , 2021.
Synthetic Transition from Thiourea-Based Compounds to Tetrazole Derivatives: Structure and Biological Evaluation of Synthesized New N-(Furan-2-ylmethyl)-1H-tetrazol-5-amine DerivativesSzulczyk, D. et al.Molecules 26, , 2021.
2020
Computational reconstruction of atomistic protein structures from coarse-grained modelsBadaczewska-Dawid, A.E., Koliński, A. & Kmiecik, S.Computational and Structural Biotechnology Journal 18, 162-176, 2020.
Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulationKoliński, M. et al.International Journal of Biological Macromolecules 149, 1151-1160, 2020.
Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinementBadaczewska-Dawid, A.E., Kmiecik, S. & Kolinski, M.Briefings in Bioinformatics , 2020.
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.
Isoxazole-containing 5′ mRNA cap analogues as inhibitors of the translation initiation processPiecyk, K. et al.Bioorganic Chemistry 96, 103583, 2020.
Phosphorylation of the N-terminal domain of ribosomal P-stalk protein uL10 governs its association with the ribosomeFilipek, K., Michalec-Wawiórka, B., Boguszewska, A., Kmiecik, S. & Tchórzewski, M.FEBS Letters 594, 3002-3019, 2020.
Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex StructuresBadaczewska-Dawid, A.E., Khramushin, A., Koliński, A., Schueler-Furman, O. & Kmiecik, S.Protein Structure Prediction 273–287, 2020.
Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASSBadaczewska-Dawid, A.E., Koliński, A. & Kmiecik, S.Protein Structure Prediction 337–353, 2020.
2019
Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubilityKuriata, A. et al.Nucleic Acids Research 47, W300-W307, 2019.
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 standalone: a toolbox for flexible protein-peptide dockingCiemny, M. et al.Bioinformatics btz185, , 2019.
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.
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.
Protein Dynamics Simulations Using Coarse-Grained ModelsKmiecik, S., Wabik, J., Kolinski, M., Kouza, M. & Koliński, A.Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 61–87, 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.
CABS-flex standalone: a simulation environment for fast modeling of protein flexibilityKurcinski, M. et al.Bioinformatics bty685, 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.
Design and synthesis of novel 1H-tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studiesSzulczyk, D. et al.European Journal of Medicinal Chemistry 156, 631 - 640, 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.
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.

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