Publications
Pages
Conservation of complex knotting and slipknotting patterns in proteins.Proceedings of the National Academy of Sciences of the United States of America 109, E1715-23, 2012.
Energy landscape of knotted protein folding.Proceedings of the National Academy of Sciences of the United States of America 109, 17783-8, 2012.
Genomics-aided structure prediction.Proceedings of the National Academy of Sciences of the United States of America 109, 10340-5, 2012.
CABS-NMR–De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl NOEsJournal of c\Computational Chemistry 32, 536–44, 2011.
Velocity scaling for optimizing replica exchange molecular dynamicsThe Journal of Chemical Physics 134, 044124, 2011.
Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulationsThe Journal of Chemical Physics 132, 165104, 2010.
TRACER. A new approach to comparative modeling that combines threading with free-space conformational samplingActa Biochimica Polonica 57, 125–33, 2010.
Dependence of protein mechanical unfolding pathways on pulling speedsThe Journal of Chemical Physics 130, 145102, 2009.
Distance matrix-based approach to protein structure predictionJournal of Structural and Functional Genomics 10, 67–81, 2009.
Dodging the crisis of folding proteins with knots.Proceedings of the National Academy of Sciences of the United States of America 106, 3119-24, 2009.
Mechanical strength of 17,134 model proteins and cysteine slipknots.PLoS Comput Biol 5, e1000547, 2009.
Protein mechanical unfolding: Importance of non-native interactionsThe Journal of Chemical Physics 131, 215103, 2009.
On the remarkable mechanostability of scaffoldins and the mechanical clamp motif.Proceedings of the National Academy of Sciences of the United States of America 106, 13791-6, 2009.
Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained modelsBMC Structural Biology 8, 36, 2008.
Fast and accurate methods for predicting short-range constraints in protein modelsJournal of Computer-Aided Molecular Design 22, 783–8, 2008.
New force replica exchange method and protein folding pathways probed by force-clamp techniqueThe Journal of Chemical Physics 128, 045103, 2008.