Andrzej Kolinski Research Group

Coarse-grained protein modeling

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2-Methylene analogs of 1alpha-hydroxy-19-norvitamin D3: synthesis, biological activities and docking to the ligand binding domain of the rat vitamin D receptorGrzywacz, P. et al.The Journal of Steroid Biochemistry and Molecular Biology 89-90, 13-7, 2004.
A
An algorithm for prediction of structural elements in small proteinsKoliński, A., Skolnick, J. & Godzik, A.Proceeding of I-st Pacific Symposium on Biocomputing 446–460, 1996.
Are proteins ideal mixtures of amino acids? Analysis of energy parameter setsGodzik, A., Koliński, A. & Skolnick, J.Protein Science: a Publication of the Protein Society 4, 2107–2117, 1995.
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.
B
Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinatesGront, D., Kmiecik, S. & Koliński, A.Journal of Computational Chemistry 28, 1593–7, 2007.
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.
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.
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.Gniewek, P., Koliński, A., Kloczkowski, A. & Gront, D.BMC Bioinformatics 15, 22, 2014.
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.Gniewek, P., Koliński, A., Kloczkowski, A. & Gront, D.BMC Bioinformatics 15, 22, 2014.
BioShell–a package of tools for structural biology computationsGront, D. & Koliński, A.Bioinformatics (Oxford, England) 22, 621–622, 2006.
C
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structuresKuriata, A. et al.Nucleic Acids Research, gky356 , 2018.
Chameleonicity and folding of the C-fragment of TOP7Gaye, M.L., Hardwick, C., Kouza, M. & Hansmann, U.H.E.EPL (Europhysics Letters) 97, 68003, 2012.
Clustering as a supporting tool for structural drug designGront, D., Kurcinski, M. & Koliński, A.Acta Poloniae Pharmaceutica. Drug Research 63, 436-8, 2006.
Coarse-grained modeling of mucus barrier propertiesGniewek, P. & Koliński, A.Biophysical Journal 102, 195–200, 2012.
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.
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamicsGniewek, P. & Koliński, A.Biophysical Journal 99, 3507–16, 2010.
Coarse-Grained Protein Models and Their ApplicationsKmiecik, S. et al.Chemical Reviews 116, 7898–7936, 2016.
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.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular DynamicsWabik, J., Kmiecik, S., Gront, D., Kouza, M. & Koliński, A.International Journal of Molecular Sciences 14, 9893–9905, 2013.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityGil-Garcia, M. et al.Molecular Pharmaceutics 15, 3846-3859, 2018.
Comparative modeling without implicit sequence alignmentsKoliński, A. & Gront, D.Bioinformatics (Oxford, England) 23, 2522–7, 2007.
Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energyGront, D., Koliński, A. & Skolnick, J.Journal of Chemical Physics 113, 5065–5071, 2000.
Computer design of idealized beta-motifsKoliński, A., Galazka, W. & Skolnick, J.Journal of Chemical Physics 103, 10286–10297, 1995.
Contact mapKoliński, A., Godzik, A. & Skolnick, J.Encyclopedia of Molecular Biology 567–571, 1999.

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