Publications
Pages
Why do proteins divide into domains? Insights from lattice model simulationsBiomacromolecules 8, 3519–24, 2007.
Velocity scaling for optimizing replica exchange molecular dynamicsThe Journal of Chemical Physics 134, 044124, 2011.
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced modelBiophysical Journal 85, 3271–3278, 2003.
TRACER. A new approach to comparative modeling that combines threading with free-space conformational samplingActa Biochimica Polonica 57, 125–33, 2010.
T-Pile–a package for thermodynamic calculations for biomoleculesBioinformatics (Oxford, England) 23, 1840–1842, 2007.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force fieldBMC Structural Biology 7, 43, 2007.
TOUCHSTONE II: a new approach to ab initio protein structure predictionBiophysical Journal 85, 1145–64, 2003.
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraintsProceedings of the National Academy of Sciences of the United States of America 98, 10125–30, 2001.
Static and dynamic properties of a new lattice model of polypeptide chainsThe Journal of Chemical Physics 94, 3978, 1991.
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transitionBiopolymers 69, 399–405, 2003.
Selection of optimal variants of Gō-like models of proteins through studies of stretching.Biophys J 95, 3174-91, 2008.
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.
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.
Protein structure prediction: combining de novo modeling with sparse experimental dataJournal of Computational Chemistry 28, 1668–76, 2007.
Protein modeling with reduced representation: statistical potentials and protein folding mechanismActa Biochimica Polonica 52, 741–8, 2005.
Protein modeling and structure prediction with a reduced representationActa Biochimica Polonica 51, 349–71, 2004.
Protein mechanical unfolding: Importance of non-native interactionsThe Journal of Chemical Physics 131, 215103, 2009.
Protein fragment reconstruction using various modeling techniquesJournal of Computer-Aided Molecular Design 17, 725–38, 2003.
Protein Folding with a Reduced Model and Inaccurate Short-Range RestraintsMacromolecular Theory and Simulations 14, 444–451, 2005.