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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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.
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.
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.
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.
Protein-peptide docking: opportunities and challengesCiemny, M.Pawel et al.Drug Discovery Today 23, 1530-1537, 2018.
Protein–peptide docking using CABS-dock and contact informationBlaszczyk, M., Ciemny, M., Koliński, A., Kurcinski, M. & Kmiecik, S.Briefings in Bioinformatics bby080, 2018.
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.
Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper(II) complexes of 1,3-disubstituted thiourea ligandsBielenica, A. et al.Journal of Inorganic Biochemistry 182, 61 - 70, 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.
Fast and Accurate Accessible Surface Area Prediction Without a Sequence ProfileFaraggi, E., Kouza, M., Zhou, Y. & Kloczkowski, A.Methods in Molecular Biology 1484, 127-136, 2017.
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.

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