Andrzej Kolinski Research Group

Coarse-grained protein modeling

Read our new review on coarse-grained modeling

Modeling Software & Servers

Try the CABSdock for protein-peptide docking

Biomolecules — dynamics & interactions

Read relevant publications
0
-1
-2
-3
Previous Pause Next

Publications

Export 69 results:
Author Title Type [ Year(Asc)]
Filters: Keyword is Proteins  [Clear All Filters]

Pages

2008
Predicting the order in which contacts are broken during single molecule protein stretching experiments.Sulkowska, J.I., Kloczkowski, A., Sen, T.Z., Cieplak, M. & Jernigan, R.L.Proteins 71, 45-60, 2008.
Selection of optimal variants of Gō-like models of proteins through studies of stretching.Sulkowska, J.I. & Cieplak, M.Biophys J 95, 3174-91, 2008.
Stretching to understand proteins - a survey of the protein data bank.Sulkowska, J.I. & Cieplak, M.Biophys J 94, 6-13, 2008.
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.
Characterization of protein-folding pathways by reduced-space modelingKmiecik, S. & Koliński, A.Proceedings of the National Academy of Sciences of the United States of America 104, 12330–5, 2007.
Comparative modeling without implicit sequence alignmentsKoliński, A. & Gront, D.Bioinformatics (Oxford, England) 23, 2522–7, 2007.
Hierarchical modeling of protein interactionsKurcinski, M. & Koliński, A.Journal of Molecular Modeling 13, 691–698, 2007.
Protein structure prediction: combining de novo modeling with sparse experimental dataLatek, D., Ekonomiuk, D. & Koliński, A.Journal of Computational Chemistry 28, 1668–76, 2007.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force fieldKmiecik, S., Gront, D. & Koliński, A.BMC Structural Biology 7, 43, 2007.
T-Pile–a package for thermodynamic calculations for biomoleculesGront, D. & Koliński, A.Bioinformatics (Oxford, England) 23, 1840–1842, 2007.
Why do proteins divide into domains? Insights from lattice model simulationsRutkowska, A. & Koliński, A.Biomacromolecules 8, 3519–24, 2007.
2006
BioShell–a package of tools for structural biology computationsGront, D. & Koliński, A.Bioinformatics (Oxford, England) 22, 621–622, 2006.
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.
A minimal proteinlike lattice model: an alpha-helix motifPokarowski, P., Droste, K. & Koliński, A.The Journal of Chemical Physics 122, 214915, 2005.
A new approach to prediction of short-range conformational propensities in proteinsGront, D. & Koliński, A.Bioinformatics (Oxford, England) 21, 981–987, 2005.
Protein Folding with a Reduced Model and Inaccurate Short-Range RestraintsPlewczynska, D. & Koliński, A.Macromolecular Theory and Simulations 14, 444–451, 2005.
Protein modeling with reduced representation: statistical potentials and protein folding mechanismEkonomiuk, D., Kielbasinski, M. & Koliński, A.Acta Biochimica Polonica 52, 741–8, 2005.
Thermal unfolding of proteins.Cieplak, M. & Sulkowska, J.I.J Chem Phys 123, 194908, 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.

Pages