Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Publications

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2011
Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization stepSteczkiewicz, K. et al.Proceedings of the National Academy of Sciences of the United States of America 108, 9443–8, 2011.
Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanismKmiecik, S. & Koliński, A.Journal of the American Chemical Society 133, 10283–9, 2011.
2010
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamicsGniewek, P. & Koliński, A.Biophysical Journal 99, 3507–16, 2010.
Modeling of loops in proteins: a multi-method approachJamroz, M. & Koliński, A.BMC Structural Biology 10, 5, 2010.
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acidKurcinski, M. & Koliński, A.The Journal of Steroid Biochemistry and Molecular Biology 121, 124–9, 2010.
2008
Folding pathway of the b1 domain of protein G explored by multiscale modelingKmiecik, S. & Koliński, A.Biophysical Journal 94, 726–36, 2008.
2007
Characterization of protein-folding pathways by reduced-space modelingKmiecik, S. & Koliński, A.Proceedings of the National Academy of Sciences of the United States of America 104, 12330–5, 2007.
Hierarchical modeling of protein interactionsKurcinski, M. & Koliński, A.Journal of Molecular Modeling 13, 691–698, 2007.
Protein structure prediction: combining de novo modeling with sparse experimental dataLatek, D., Ekonomiuk, D. & Koliński, A.Journal of Computational Chemistry 28, 1668–76, 2007.
Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequencesKurcinski, M. & Koliński, A.The Journal of Steroid Biochemistry and Molecular Biology 103, 357–60, 2007.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force fieldKmiecik, S., Gront, D. & Koliński, A.BMC Structural Biology 7, 43, 2007.
Why do proteins divide into domains? Insights from lattice model simulationsRutkowska, A. & Koliński, A.Biomacromolecules 8, 3519–24, 2007.
2005
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of modelsKoliński, A. & Bujnicki, J.M.Proteins 61 Suppl. 7, 84–90, 2005.
A minimal proteinlike lattice model: an alpha-helix motifPokarowski, P., Droste, K. & Koliński, A.The Journal of Chemical Physics 122, 214915, 2005.
2004
Protein modeling and structure prediction with a reduced representationKoliński, A.Acta Biochimica Polonica 51, 349–71, 2004.
2003
A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native statePokarowski, P., Koliński, A. & Skolnick, J.Biophysical Journal 84, 1518–26, 2003.
Protein fragment reconstruction using various modeling techniquesBoniecki, M., Rotkiewicz, P., Skolnick, J. & Koliński, A.Journal of Computer-Aided Molecular Design 17, 725–38, 2003.
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transitionKoliński, A., Gront, D., Pokarowski, P. & Skolnick, J.Biopolymers 69, 399–405, 2003.
TOUCHSTONE: a unified approach to protein structure prediction.Skolnick, J. et al.Proteins CASP Suppl, 469–79, 2003.
TOUCHSTONE II: a new approach to ab initio protein structure predictionZhang, Y., Koliński, A. & Skolnick, J.Biophysical Journal 85, 1145–64, 2003.
2002
A unified approach to the prediction of protein structure and functionSkolnick, J. & Koliński, A.Computational Methods for Protein Folding 120, , 2002.
2001
Model of three-dimensional structure of vitamin D receptor and its binding mechanism with 1alpha,25-dihydroxyvitamin D(3)Rotkiewicz, P., Sicinska, W., Koliński, A. & DeLuca, H.F.Proteins 44, 188–199, 2001.
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamicsBujnicki, J.M., Rotkiewicz, P., Koliński, A. & Rychlewski, L.Protein Engineering 14, 717–721, 2001.
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraintsKihara, D., Lu, H., Koliński, A. & Skolnick, J.Proceedings of the National Academy of Sciences of the United States of America 98, 10125–30, 2001.
2000
Computer simulations of the properties of the alpha2, alpha2C, and alpha2D de novo designed helical proteinsSikorski, A., Koliński, A. & Skolnick, J.Proteins 38, 17–28, 2000.

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