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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Book Chapter
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.
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.
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.
Template-free predictions of three-dimensional protein structures: From first principles to knowledge-based potentialsGront, D., Latek, D., Kurcinski, M., Koliński, A. & Bujnicki, J.M.Prediction of Protein Structures, Functions, and Interactions 117-142, 2008.
Wieloskalowe modelowanie białek (Multiscale protein modeling)Gront, D. et al.Na pograniczu chemii i biologii (At the treshold of chemistry and biology) 17, 239-256, 2008.
Conference Proceedings
Coarse-grained modeling of protein structure, dynamics and protein-protein interactionsKoliński, A. et al.TASK Quarterly 18, 219–229, 2014.
Coarse-grained Protein Modeling: Dynamics, Folding Pathways and Mechanical UnfoldingKoliński, A., Blaszczyk, M. & Kmiecik, S.From Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 83–90, 2012.
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.
Prediction of Experimental Phi Values in Protein Folding by Simulation with Knowledge-based Potentials: B Domain of Protein AKmiecik, S., Blaszczyk, M. & Koliński, A.From Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 79–82, 2012.
Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.Vieth, M. et al.Proceeding of I-st Pacific Symposium on Biocomputing 653–662, 1996.
Protein Structure Prediction Using CABS – A Consensus ApproachBlaszczyk, M., Jamroz, M., Gront, D. & Koliński, A.From Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 29–32, 2012.
Journal Article
14N NMR nuclear shielding and the electronic structure of dibenzo[1,3a,4,6a]tetrazapentaleneWitanowski, M., Sitkowski, J., Sicinska, W., Biernat, S. & Webb, G.A.Magnetic Resonance in Chemistry 27, 88–91, 1989.
5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1,3-disubstituted thiourea derivativesBielenica, A. et al.European Journal of Medicinal Chemistry 116, 173–186, 2016.
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinementSkolnick, J. et al.Proteins 45, 149–156, 2001.
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinementSkolnick, J. et al.Proteins 45, 149–156, 2001.
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution modelsFeig, M., Rotkiewicz, P., Koliński, A., Skolnick, J. & Brooks, III, C.L.Proteins 41, 86–97, 2000.
Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2aHorwacik, I. et al.International Journal of Molecular Medicine 28, 47–57, 2011.
Assessing energy functions for flexible dockingVieth, M., Hirst, J.D., Koliński, A. & Brooks, III, C.L.Journal of Computational Chemistry 19, 1612–1622, 1999.
Assessment of Solvent-Induced Nitrogen Shielding Variations of Triazole SystemsWitanowski, M., Sicinska, W., Biedrzycka, Z., Grabowski, Z. & Webb, G.A.Journal of Magnetic Resonance, Series A 112, 66 - 71, 1995.
Assignments of nitrogen NMR shieldings in azine heterocycles by means of a self-adjusting linear system of incremensWitanowski, M., Sicinska, W. & Biernat, S.International Journal of Spectroscopy 7, 315-324, 1989.
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.
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.
CABS-dock standalone: a toolbox for flexible protein-peptide dockingCiemny, M. et al.Bioinformatics btz185, , 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.
CABS-fold: server for the de novo and consensus-based prediction of protein structureBlaszczyk, M., Jamroz, M., Kmiecik, S. & Koliński, A.Nucleic Acids Research 41, W406-W411, 2013.

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