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.
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.
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.
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.
A Topology Fingerprint Approach to the Inverse Protein Folding ProblemGodzik, A., Skolnick, J. & Koliński, A.Journal of Molecular Biology 227, 227–238, 1992.
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.

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