Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

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Publications

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Book
Lattice models of protein folding. Dynamics and thermodynamicsKoliński, A. & Skolnick, J.Lattice models of protein folding. Dynamics and thermodynamics, Austin, TX, Chapman & Hall. (Chapman & Hall.: Austin, TX, 1996).
Book Chapter
Ab initio modelingSkolnick, J. et al.Structural Genomics and High Throughput Structural Biology 137-162, 2006.
Application of reduced models to protein structure predictionSkolnick, J., Koliński, A. & Ortiz, A.R.Theoretical and Computational Chemistry: Computational Molecular Biology 8, 397–440, 1999.
Coarse-Grained Modeling of Protein DynamicsKmiecik, S., Wabik, J., Kolinski, M., Kouza, M. & Koliński, A.Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed. 1, 55-79, 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.
Contact mapKoliński, A., Godzik, A. & Skolnick, J.Encyclopedia of Molecular Biology 567–571, 1999.
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.
Lattice polymers and protein modelsKoliński, A. & Koliński, A.Multiscale Approaches to Protein Modeling 1-20, 2011.
Monte Carlo approaches to the protein folding problemSkolnick, J. & Koliński, A.Advances in Chemical Physics: Monte Carlo Methods in Chemical Physics 105, 203–242, 1999.
Monte Carlo lattice dynamics and the prediction of protein foldsSkolnick, J., Koliński, A., van Gunsteren, W.F., Weiner, P.K. & Wilkinson, A.J.Computer Simulations of Biomolecular Systems. Theoretical and Experimental Applications pp, 395–429, 1997.
Multiscale approach to protein folding dynamicsKmiecik, S., Jamroz, M., Koliński, A. & Koliński, A.Multiscale Approaches to Protein Modeling 281-294, 2011.
Multiscale protein and peptide dockingKurcinski, M., Jamroz, M. & Koliński, A.Multiscale Approaches to Protein Modeling 21-34, 2011.
PrefaceKoliński, A. & Koliński, A.Multiscale Approaches to Protein Modeling , 2011.
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.
Protocols for efficient simulations of long time protein dynamics using coarse-grained CABS modelJamroz, M., Koliński, A. & Kmiecik, S.Protein structure prediction (3rd Edition), Methods in Molecular Biology, Daisuke Kihara, Ed. 1137, 235-250, 2014.
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.

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