Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Publications

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2-Methylene analogs of 1alpha-hydroxy-19-norvitamin D3: synthesis, biological activities and docking to the ligand binding domain of the rat vitamin D receptorGrzywacz, P. et al.The Journal of Steroid Biochemistry and Molecular Biology 89-90, 13-7, 2004.
High throughput method for protein structure predictionGront, D. et al.NIC Workshop 2006: From Computational Biophysics to System Biology 34, 79-82, 2006.
T-Pile–a package for thermodynamic calculations for biomoleculesGront, D. & Koliński, A.Bioinformatics (Oxford, England) 23, 1840–1842, 2007.
Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinatesGront, D., Kmiecik, S. & Koliński, A.Journal of Computational Chemistry 28, 1593–7, 2007.
Clustering as a supporting tool for structural drug designGront, D., Kurcinski, M. & Koliński, A.Acta Poloniae Pharmaceutica. Drug Research 63, 436-8, 2006.
Utility library for structural bioinformaticsGront, D. & Koliński, A.Bioinformatics (Oxford, England) 24, 584–5, 2008.
Fast and accurate methods for predicting short-range constraints in protein modelsGront, D. & Koliński, A.Journal of Computer-Aided Molecular Design 22, 783–8, 2008.
Modeling Protein Structures and their Complexes with Sparse Experimental DataGront, D., Blaszczyk, M., Wabik, J. & Koliński, A.From Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 49–52, 2012.
Efficient scheme for optimization of parallel tempering Monte Carlo methodGront, D. & Koliński, A.Journal of Physics: Condensed Matter 19, , 2007.
Exploring protein energy landscapes with hierarchical clusteringGront, D., Hansmann, U.H.E. & Koliński, A.International Journal of Quantum Chemistry 105, 826–830, 2005.
HCPM–program for hierarchical clustering of protein modelsGront, D. & Koliński, A.Bioinformatics 21, 3179–80, 2005.
BioShell–a package of tools for structural biology computationsGront, D. & Koliński, A.Bioinformatics (Oxford, England) 22, 621–622, 2006.
Protein structure prediction by tempering spatial constraintsGront, D., Koliński, A. & Hansmann, U.H.E.Journal of Computer-Aided Molecular Design 19, 603–8, 2005.
Template-free predictions of three-dimensional protein structures: From first principles to knowledge-based potentialsGront, D., Latek, D., Kurcinski, M., Koliński, A. & Bujnicki, J.M.Prediction of Protein Structures, Functions, and Interactions 117-142, 2008.
Optimization of protein modelsGront, D., Kmiecik, S., Blaszczyk, M., Ekonomiuk, D. & Koliński, A.Wiley Interdisciplinary Reviews: Computational Molecular Science 2, 479–493, 2012.
A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamicsGront, D., Koliński, A. & Skolnick, J.The Journal of Chemical Physics 115, 1569–1574, 2001.
Wieloskalowe modelowanie białek (Multiscale protein modeling)Gront, D. et al.Na pograniczu chemii i biologii (At the treshold of chemistry and biology) 17, 239-256, 2008.
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profilesGront, D., Blaszczyk, M., Wojciechowski, P. & Koliński, A.Nucleic Acids Research 40, W257–62, 2012.
Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energyGront, D., Koliński, A. & Skolnick, J.Journal of Chemical Physics 113, 5065–5071, 2000.
A new approach to prediction of short-range conformational propensities in proteinsGront, D. & Koliński, A.Bioinformatics (Oxford, England) 21, 981–987, 2005.
Regularities in interaction patterns of globular proteinsGodzik, A., Skolnick, J. & Koliński, A.Protein Engineering 6, 801–810, 1993.
Lattice representations of globular proteins: How good are they?Godzik, A., Koliński, A. & Skolnick, J.Journal of Computational Chemistry 14, 1194-1202 , 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.
Simulations of the Folding Pathway of TIM-type a/ß Barrel ProteinsGodzik, A., Skolnick, J. & Koliński, A.Proceedings of the National Academy of Sciences of the United States of America 89, 2629–2633, 1992.
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.

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