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Coarse-grained protein modeling

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Publications

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Chameleonicity and folding of the C-fragment of TOP7Gaye, M.L., Hardwick, C., Kouza, M. & Hansmann, U.H.E.EPL (Europhysics Letters) 97, 68003, 2012.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityGil-Garcia, M. et al.Molecular Pharmaceutics 15, 3846-3859, 2018.
Optimization of profile-to-profile alignment parameters for one-dimensional threadingGniewek, P., Koliński, A. & Gront, D.Journal of Computational Biology 19, 879–86, 2012.
How noise in force fields can affect the structural refinement of protein models?Gniewek, P., Koliński, A., Jernigan, R.L. & Kloczkowski, A.Proteins 80, 335–341, 2012.
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamicsGniewek, P. & Koliński, A.Biophysical Journal 99, 3507–16, 2010.
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.Gniewek, P., Koliński, A., Kloczkowski, A. & Gront, D.BMC Bioinformatics 15, 22, 2014.
Note: A simple picture of subdiffusive polymer motion from stochastic simulationsGniewek, P. & Koliński, A.The Journal of Chemical Physics 134, 056101, 2011.
Coarse-grained modeling of mucus barrier propertiesGniewek, P. & Koliński, A.Biophysical Journal 102, 195–200, 2012.
Elastic network normal modes provide a basis for protein structure refinementGniewek, P., Koliński, A., Jernigan, R.L. & Kloczkowski, A.The Journal of Chemical Physics 136, 195101, 2012.
Multibody coarse-grained potentials for native structure recognition and quality assessment of protein modelsGniewek, P., Leelananda, S.P., Koliński, A., Jernigan, R.L. & Kloczkowski, A.Proteins 79, 1923–9, 2011.
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.
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.
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.

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