Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Publications

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2005
Protein modeling with reduced representation: statistical potentials and protein folding mechanismEkonomiuk, D., Kielbasinski, M. & Koliński, A.Acta Biochimica Polonica 52, 741–8, 2005.
Protein structure prediction by tempering spatial constraintsGront, D., Koliński, A. & Hansmann, U.H.E.Journal of Computer-Aided Molecular Design 19, 603–8, 2005.
Theoretical model of prion propagation: a misfolded protein induces misfoldingMałolepsza, E., Boniecki, M., Koliński, A. & Piela, L.Proceedings of the National Academy of Sciences of the United States of America 102, 7835–40, 2005.
Thermal unfolding of proteins.Cieplak, M. & Sulkowska, J.I.J Chem Phys 123, 194908, 2005.
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.
Solvent polarity and hydrogen-bonding effects on the nitrogen NMR shieldings of N-nitrosamines and DFT calculations of the shieldings of C-, N-, and O-nitroso systemsWitanowski, M., Biedrzycka, Z., Sicinska, W. & Grabowski, Z.Journal of Magnetic Resonance 164, 212-9, 2003.
TOUCHSTONE II: a new approach to ab initio protein structure predictionZhang, Y., Koliński, A. & Skolnick, J.Biophysical Journal 85, 1145–64, 2003.
2002
Computer simulations of protein folding with a small number of distance restraintsSikorski, A., Koliński, A. & Skolnick, J.Acta Biochimica Polonica 49, 683–692, 2002.
2001
Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinementKoliński, A., Betancourt, M., Kihara, D., Rotkiewicz, P. & Skolnick, J.Proteins 44, 133–149, 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.
Structural genomics and its importance for gene function analysisSkolnick, J., Fetrow, J.S. & Koliński, A.Nature Biotechnology 18, 283–287, 2000.
1999
De novo simulations of the folding thermodynamics of the GCN4 leucine zipperMohanty, D., Koliński, A. & Skolnick, J.Biophysical Journal 77, 54–69, 1999.
A method for the improvement of threading-based protein modelsKoliński, A., Rotkiewicz, P., Ilkowski, B. & Skolnick, J.Proteins 37, 592–610, 1999.
1998
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo modelKoliński, A. & Skolnick, J.Proteins 32, 475–494, 1998.
Computer simulations of de novo designed helical proteinsSikorski, A., Koliński, A. & Skolnick, J.Biophysical Journal 75, 92–105, 1998.
1997
MONSSTER: a method for folding globular proteins with a small number of distance restraintsSkolnick, J., Koliński, A. & Ortiz, A.R.Journal of Molecular Biology 265, 217–241, 1997.
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.
Folding simulations and computer redesign of protein A three-helix bundle motifsOlszewski, K.A., Koliński, A. & Skolnick, J.Proteins 25, 286–299, 1996.
On the origin of the cooperativity of protein folding: implications from model simulationsKoliński, A., Galazka, W. & Skolnick, J.Proteins 26, 271–287, 1996.
1995
Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipperVieth, M., Koliński, A., Brooks, III, C.L. & Skolnick, J.Journal of Molecular Biology 251, 448–67, 1995.
1994
Monte Carlo simulations of protein folding. I. Lattice model and interaction schemeKoliński, A. & Skolnick, J.Proteins 18, 338-52, 1994.

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