Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Publications

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Filters: Keyword is Proteins: chemistry  [Clear All Filters]

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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.
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.

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