Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Biomolecules — dynamics & interactions

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Publications

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Author Title [ Type(Desc)] Year
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Book Chapter
Monte Carlo lattice dynamics and the prediction of protein foldsSkolnick, J., Koliński, A., van Gunsteren, W.F., Weiner, P.K. & Wilkinson, A.J.Computer Simulations of Biomolecular Systems. Theoretical and Experimental Applications pp, 395–429, 1997.
Conference Proceedings
Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.Vieth, M. et al.Proceeding of I-st Pacific Symposium on Biocomputing 653–662, 1996.
Journal Article
Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubilityKuriata, A. et al.Nucleic Acids Research 47, W300-W307, 2019.
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structuresZambrano, R. et al.Nucleic Acids Research 43 (W1), W306-W313, 2015.
Aggrescan3D standalone package for structure-based prediction of protein aggregation propertiesKuriata, A., Iglesias, V., Kurcinski, M., Ventura, S. & Kmiecik, S.Bioinformatics btz143, , 2019.
Assessing energy functions for flexible dockingVieth, M., Hirst, J.D., Koliński, A. & Brooks, III, C.L.Journal of Computational Chemistry 19, 1612–1622, 1999.
Collapse Transition of Semiflexible Polymers in 2-dimensional SystemsKoliński, A., Vieth, M. & Sikorski, A.Acta Physica Polonica 79, 601-612, 1991.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityGil-Garcia, M. et al.Molecular Pharmaceutics 15, 3846-3859, 2018.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityGil-Garcia, M. et al.Molecular Pharmaceutics 15, 3846-3859, 2018.
De novo simulations of the folding of GCN4 and its mutantsSkolnick, J., Vieth, M., Koliński, A. & Brooks, III, C.L.Modeling of Biomolecular Structures and Mechanisms 8, 95–98, 1995.
A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutantsVieth, M., Koliński, A., Brooks, III, C.L. & Skolnick, J.DIMACS Series in Discrete Mathematics and Theoretical Computer Science 23, 233–236, 1996.
Key Factors Governing Fibril Formation Of Proteins: Insights From Simulations And ExperimentsCo, N.Truong, Viet, M.Hoang, Truong, P.Minh, Kouza, M. & Li, M.SuanTask Quarterly 18, 245–254, 2014.
Method for predicting the state of association of discretized protein models. Application to leucine zippers.Vieth, M., Koliński, A. & Skolnick, J.Biochemistry 35, 955–967, 1996.
Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipperViñals, J., Koliński, A. & Skolnick, J.Biophysical Journal 83, 2801–2811, 2002.
Prediction of protein secondary structure by an enhanced neural networkVieth, M. & Koliński, A.Acta Biochimica Polonica 38, , 1991.
Prediction of protein secondary structure by neural networks: encoding short and long range patterns of amino acid packingVieth, M., Koliński, A., Skolnick, J. & Sikorski, A.Acta Biochimica Polonica 39, 369–392, 1992.
Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipperVieth, M., Koliński, A., Brooks, III, C.L. & Skolnick, J.Journal of Molecular Biology 251, 448–67, 1995.
Prediction of the Folding Pathways and Structure of the GCN4 Leucine ZipperVieth, M., Koliński, A., Brooks, III, C.L. & Skolnick, J.Journal of Molecular Biology 237, 361 - 367, 1994.
On the remarkable mechanostability of scaffoldins and the mechanical clamp motif.Valbuena, A. et al.Proceedings of the National Academy of Sciences of the United States of America 106, 13791-6, 2009.
On the remarkable mechanostability of scaffoldins and the mechanical clamp motif.Valbuena, A. et al.Proceedings of the National Academy of Sciences of the United States of America 106, 13791-6, 2009.
A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulationsVieth, M., Koliński, A. & Skolnick, J.Journal of Chemical Physics 102, 6189–6193, 1995.
A Stevedore's protein knot.Bölinger, D. et al.PLoS Comput Biol 6, e1000731, 2010.
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.
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.