Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Publications

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2003
TOUCHSTONEX: protein structure prediction with sparse NMR dataLi, W. et al.Proteins 53, 290-306, 2003.
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced modelKoliński, A., Klein, P., Romiszowski, P. & Skolnick, J.Biophysical Journal 85, 3271–3278, 2003.
2002
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genomeKihara, D., Zhang, Y., Lu, H., Koliński, A. & Skolnick, J.Proceedings of the National Academy of Sciences of the United States of America 99, 5993–5998, 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
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution modelsFeig, M., Rotkiewicz, P., Koliński, A., Skolnick, J. & Brooks, III, C.L.Proteins 41, 86–97, 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.
1999
Ab initio folding of proteins using restraints derived from evolutionary informationOrtiz, A.R., Koliński, A., Rotkiewicz, P., Ilkowski, B. & Skolnick, J.Proteins Suppl. 3, 177–185, 1999.
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniquesKoliński, A., Ilkowski, B. & Skolnick, J.Biophysical Journal 77, 2942–52, 1999.
A method for the improvement of threading-based protein modelsKoliński, A., Rotkiewicz, P., Ilkowski, B. & Skolnick, J.Proteins 37, 592–610, 1999.
1998
Computer simulations of de novo designed helical proteinsSikorski, A., Koliński, A. & Skolnick, J.Biophysical Journal 75, 92–105, 1998.
1997
Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turnsHu, W.-P., Koliński, A. & Skolnick, J.Proteins 29, 443–460, 1997.
A method for the prediction of surface "U"-turns and transglobular connections in small proteinsKoliński, A., Skolnick, J., Godzik, A. & Hu, W.-P.Proteins 27, 290–308, 1997.
1995
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.
1993
From independent modules to molten globules: observations on the nature of protein folding intermediatesSkolnick, J., Koliński, A. & Godzik, A.Proceedings of the National Academy of Sciences of the United States of America 90, 2099–100, 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
Static and dynamic properties of a new lattice model of polypeptide chainsKoliński, A., Milik, M. & Skolnick, J.The Journal of Chemical Physics 94, 3978, 1991.
1989
Monte Carlo studies on equilibrium globular protein folding. II. Beta-barrel globular protein modelsSkolnick, J., Koliński, A. & Yaris, R.Biopolymers 28, 1059–95, 1989.
1987
Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of beta-barrel proteinsKoliński, A., Skolnick, J. & Yaris, R.Biopolymers 26, 937–62, 1987.

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