Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Publications

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2018
Design and synthesis of novel 1H-tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studiesSzulczyk, D. et al.European Journal of Medicinal Chemistry 156, 631 - 640, 2018.
2013
Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structureSaraswathi, S., Fernández-Martínez, J.L., Koliński, A., Jernigan, R.L. & Kloczkowski, A.Journal of Molecular Modeling 19, 4337-48, 2013.
2009
Dependence of protein mechanical unfolding pathways on pulling speedsLi, M.Suan & Kouza, M.The Journal of Chemical Physics 130, 145102, 2009.
Distance matrix-based approach to protein structure predictionKloczkowski, A. et al.Journal of Structural and Functional Genomics 10, 67–81, 2009.
Dodging the crisis of folding proteins with knots.Sulkowska, J.I., Sułkowski, P. & Onuchic, J.Proceedings of the National Academy of Sciences of the United States of America 106, 3119-24, 2009.
2008
Designing an Automatic Pipeline for Protein Structure Prediction Designing an Automatic Pipeline for Protein Structure PredictionKmiecik, S. et al.From Computational Biophysics to Systems Biology (CBSB08) 40, 105–108, 2008.
2006
Denatured proteins and early folding intermediates simulated in a reduced conformational spaceKmiecik, S., Kurcinski, M., Rutkowska, A., Gront, D. & Koliński, A.Acta Biochimica Polonica 53, 131–143, 2006.
DFT Calculation of Nitrogen Chemical Shifts in the Active Site of Vitamin D ReceptorSicinska, W.Polish Journal of Chemistry Vol. 80, no 7, 1171–1183, 2006.
2005
DNA vaccine expressing the mimotope of GD2 ganglioside induces protective GD2 cross-reactive antibody responsesBolesta, E. et al.Cancer Research 65, 3410–8, 2005.
2000
Derivation of protein-specific pair potentials based on weak sequence fragment similaritySkolnick, J., Koliński, A. & Ortiz, A.Proteins: Structure, Function, Bioinformatics 38, 3–16, 2000.
1999
De novo predictions of the quaternary structure of leucine zippers and other coiled coilsSkolnick, J., Koliński, A. & Mohanty, D.International Journal of Quantum Chemistry 75, 165–176, 1999.
De novo simulations of the folding thermodynamics of the GCN4 leucine zipperMohanty, D., Koliński, A. & Skolnick, J.Biophysical Journal 77, 54–69, 1999.
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniquesKoliński, A., Ilkowski, B. & Skolnick, J.Biophysical Journal 77, 2942–52, 1999.
1997
Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?Skolnick, J., Jaroszewski, L., Koliński, A. & Godzik, A.Protein Science 6, 676–688, 1997.
Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactionsKoliński, A. & Skolnick, J.Journal of Chemical Physics 107, 953–964, 1997.
1996
A detailed 1H and 13C NMR study of a repeating disaccharide of hyaluronan: the effect of sodium and calcium ionsSicinska, W. & Lerner, L.E.Carbohydrate Research 286, 151-159, 1996.
A detailed 1H and 13C NMR study of a repeating disaccharide of hyaluronan: the effect of sodium and calcium ionsSicinska, W. & Lerner, L.E.Carbohydrate Research 286, 151 - 159, 1996.
Does a backwardly read protein sequence have a unique native state?Olszewski, K.A., Koliński, A. & Skolnick, J.Protein Engineering 9, 5–14, 1996.
1995
De novo simulations of the folding of GCN4 and its mutantsSkolnick, J., Vieth, M., Koliński, A. & Brooks, III, C.L.Modeling of Biomolecular Structures and Mechanisms 8, 95–98, 1995.
1994
De Novo Prediction of Protein Tertiary StructureSkolnick, J. & Koliński, A.Polymer Preprints 35, 82–83, 1994.
Dynamics of star branched polymers in a matrix of linear chains—a Monte Carlo studySikorski, A., Koliński, A. & Skolnick, J.Macromolecular Theory and Simulations 3, 715–729, 1994.
1993
De novo and inverse folding predictions of protein structure and dynamicsGodzik, A., Koliński, A. & Skolnick, J.Journal of Computer-Aided Molecular Design 7, 397–438, 1993.
A detailed 1H and 13C NMR study of a repeating disaccharide of hyaluronan: the effects of temperature and counterion typeSicinska, W., Adams, B. & Lerner, L.Carbohydrate Research 242, 29 - 51, 1993.
1992
Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptidesKoliński, A. & Skolnick, J.Journal of Chemical Physics 97, 9412–9426, 1992.
1991
Dinitrogen as a possible internal standard for nitrogen nuclear magnetic resonanceWitanowski, M., Sicinska, W., Biernat, S. & Webb, G.A.International Journal of Spectroscopy 9, 55-59, 1991.

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