Publications
Pages
Selection of optimal variants of Gō-like models of proteins through studies of stretching.Biophys J 95, 3174-91, 2008.
Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinatesJournal of Computational Chemistry 28, 1593–7, 2007.
Characterization of protein-folding pathways by reduced-space modelingProceedings of the National Academy of Sciences of the United States of America 104, 12330–5, 2007.
Comparative modeling without implicit sequence alignmentsBioinformatics (Oxford, England) 23, 2522–7, 2007.
Protein structure prediction: combining de novo modeling with sparse experimental dataJournal of Computational Chemistry 28, 1668–76, 2007.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force fieldBMC Structural Biology 7, 43, 2007.
T-Pile–a package for thermodynamic calculations for biomoleculesBioinformatics (Oxford, England) 23, 1840–1842, 2007.
Why do proteins divide into domains? Insights from lattice model simulationsBiomacromolecules 8, 3519–24, 2007.
BioShell–a package of tools for structural biology computationsBioinformatics (Oxford, England) 22, 621–622, 2006.
Inferring ideal amino acid interaction forms from statistical protein contact potentialsProteins 59, 49–57, 2005.
A minimal proteinlike lattice model: an alpha-helix motifThe Journal of Chemical Physics 122, 214915, 2005.
A new approach to prediction of short-range conformational propensities in proteinsBioinformatics (Oxford, England) 21, 981–987, 2005.
Protein Folding with a Reduced Model and Inaccurate Short-Range RestraintsMacromolecular Theory and Simulations 14, 444–451, 2005.
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.
A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native stateBiophysical Journal 84, 1518–26, 2003.
Protein fragment reconstruction using various modeling techniquesJournal of Computer-Aided Molecular Design 17, 725–38, 2003.
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transitionBiopolymers 69, 399–405, 2003.
TOUCHSTONE II: a new approach to ab initio protein structure predictionBiophysical Journal 85, 1145–64, 2003.