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Coarse-grained protein modeling

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Publications

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Author [ Title(Desc)] Type Year
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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.
C
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.
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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.
H
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.
K
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.
M
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.
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.
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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.
P
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.
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.
R
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.
S
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.
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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.