Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Modeling Software & Servers

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Biomolecules — dynamics & interactions

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Publications

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Author Title Type [ Year(Asc)]
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2017
Toward more efficient simulations of slow processes in large biomolecular systems: Comment on "Ligand diffusion in proteins via enhanced sampling in molecular dynamics" by Jakub Rydzewski and Wieslaw Nowak.Koliński, A.Physics of Life Reviews 22–23, 85-87, 2017.
2016
Towards protein-protein docking with significant structural changes using CABS-dockCiemny, M., Kurcinski, M., Koliński, A. & Kmiecik, S.Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 207-213, arXiv:1605.09266 , 2016.
2010
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acidKurcinski, M. & Koliński, A.The Journal of Steroid Biochemistry and Molecular Biology 121, 124–9, 2010.
TRACER. A new approach to comparative modeling that combines threading with free-space conformational samplingTrojanowski, S., Rutkowska, A. & Koliński, A.Acta Biochimica Polonica 57, 125–33, 2010.
2009
Tests of the Structure-Based Models of ProteinsCieplak, M. & Sulkowska, J.I.ACTA PHYSICA POLONICA A 115, , 2009.
2008
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.
Tightening of knots in proteins.Sulkowska, J.I., Sułkowski, P., Szymczak, P. & Cieplak, M.Phys Rev Lett 100, 058106, 2008.
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.
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamilyIbryashkina, E.M. et al.BMC Structural Biology 7, 48, 2007.
2006
Theoretical models and simulations of polymer chainsKloczkowski, A., Koliński, A. & Mark, J.E.Physical Properties of Polymers Handbook , 2006.
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitorsHoffmann, M. et al.Journal of Computer-Aided Molecular Design 20, 305–319, 2006.
2005
Theoretical model of prion propagation: a misfolded protein induces misfoldingMałolepsza, E., Boniecki, M., Koliński, A. & Piela, L.Proceedings of the National Academy of Sciences of the United States of America 102, 7835–40, 2005.
Thermal unfolding of proteins.Cieplak, M. & Sulkowska, J.I.J Chem Phys 123, 194908, 2005.
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.
TOUCHSTONEX: protein structure prediction with sparse NMR dataLi, W. et al.Proteins 53, 290-306, 2003.
2001
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamicsBujnicki, J.M., Rotkiewicz, P., Koliński, A. & Rychlewski, L.Protein Engineering 14, 717–721, 2001.
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraintsKihara, D., Lu, H., Koliński, A. & Skolnick, J.Proceedings of the National Academy of Sciences of the United States of America 98, 10125–30, 2001.
2000
Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domainYamamoto, K. et al.Proceedings of the National Academy of Sciences 97, 1467-1472, 2000.
1998
Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignmentsOrtiz, A.R., Koliński, A. & Skolnick, J.Proteins 30, 287–294, 1998.
1992
A Topology Fingerprint Approach to the Inverse Protein Folding ProblemGodzik, A., Skolnick, J. & Koliński, A.Journal of Molecular Biology 227, 227–238, 1992.