Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Biomolecules — dynamics & interactions

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Publications

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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.
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitorsHoffmann, M. et al.Journal of Computer-Aided Molecular Design 20, 305–319, 2006.
2005
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of modelsKoliński, A. & Bujnicki, J.M.Proteins 61 Suppl. 7, 84–90, 2005.
HCPM–program for hierarchical clustering of protein modelsGront, D. & Koliński, A.Bioinformatics 21, 3179–80, 2005.
Inferring ideal amino acid interaction forms from statistical protein contact potentialsPokarowski, P. et al.Proteins 59, 49–57, 2005.
Protein modeling with reduced representation: statistical potentials and protein folding mechanismEkonomiuk, D., Kielbasinski, M. & Koliński, A.Acta Biochimica Polonica 52, 741–8, 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.
2004
Protein modeling and structure prediction with a reduced representationKoliński, A.Acta Biochimica Polonica 51, 349–71, 2004.
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.
Protein fragment reconstruction using various modeling techniquesBoniecki, M., Rotkiewicz, P., Skolnick, J. & Koliński, A.Journal of Computer-Aided Molecular Design 17, 725–38, 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.
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.
Model of three-dimensional structure of vitamin D receptor and its binding mechanism with 1alpha,25-dihydroxyvitamin D(3)Rotkiewicz, P., Sicinska, W., Koliński, A. & DeLuca, H.F.Proteins 44, 188–199, 2001.
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamicsBujnicki, J.M., Rotkiewicz, P., Koliński, A. & Rychlewski, L.Protein Engineering 14, 717–721, 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.
Structural genomics and its importance for gene function analysisSkolnick, J., Fetrow, J.S. & Koliński, A.Nature Biotechnology 18, 283–287, 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.
Assessing energy functions for flexible dockingVieth, M., Hirst, J.D., Koliński, A. & Brooks, III, C.L.Journal of Computational Chemistry 19, 1612–1622, 1999.
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniquesKoliński, A., Ilkowski, B. & Skolnick, J.Biophysical Journal 77, 2942–52, 1999.

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