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Coarse-grained protein modeling

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Publications

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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.
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.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityGil-Garcia, M. et al.Molecular Pharmaceutics 15, 3846-3859, 2018.
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.

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