Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Coarse-grained simulations of membrane insertion and folding of small helical proteins using CABS modelPulawski, W., Jamroz, M., Kolinski, M., Koliński, A. & Kmiecik, S.Journal of Chemical Information and Modeling 56, 2207–2215, 2016.
Inferring ideal amino acid interaction forms from statistical protein contact potentialsPokarowski, P. et al.Proteins 59, 49–57, 2005.
A minimal proteinlike lattice model: an alpha-helix motifPokarowski, P., Droste, K. & Koliński, A.The Journal of Chemical Physics 122, 214915, 2005.
Ideal amino acid exchange forms for approximating substitution matricesPokarowski, P. et al.Proteins: Structure, Function, Bioinformatics 69, 379–393, 2007.
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.
13,13-Dimethyl-des-C,D analogues of (20S)-1α,25-dihydroxy-2-methylene-19-norvitamin D₃ (2MD): total synthesis, docking to the VDR, and biological evaluationPlonska-Ocypa, K. et al.Bioorganic & Medicinal Chemistry 19, 7205-20, 2011.
Protein Folding with a Reduced Model and Inaccurate Short-Range RestraintsPlewczynska, D. & Koliński, A.Macromolecular Theory and Simulations 14, 444–451, 2005.
Predicting real-valued protein residue fluctuation using FlexPredPeterson, L., Jamroz, M., Koliński, A. & Kihara, D.Methods in Molecular Biology 1484, 175-186, 2017.
Water Contents and Calculation of Equilibrium Constraints in Benzene Phase on System Water - Benzene - (-OH, -COOH, -NH2, -NO2, -C1) Benzene DerivativePawlowski, W. & Koliński, A.Polish Journal of Chemistry 56, 1169-1173, 1982.
Nitrogen NMR shieldings of 2-amino-5-nitro-6-methylpyridinesPalasek, B., Puszko, A., Biedrzycka, Z., Sicinska, W. & Witanowski, M.International Journal of Spectroscopy 13, 251-256, 1997.