Publications
Pages
Why do proteins divide into domains? Insights from lattice model simulationsBiomacromolecules 8, 3519–24, 2007.
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced modelBiophysical Journal 85, 3271–3278, 2003.
Uncharacterized DUF1574 leptospira proteins are SGNH hydrolasesCell Cycle (Georgetown, Tex.) 7, 542–4, 2008.
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamilyBMC Structural Biology 7, 48, 2007.
TRACER. A new approach to comparative modeling that combines threading with free-space conformational samplingActa Biochimica Polonica 57, 125–33, 2010.
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.
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitorsJournal of Computer-Aided Molecular Design 20, 305–319, 2006.
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acidThe Journal of Steroid Biochemistry and Molecular Biology 121, 124–9, 2010.
Theoretical model of prion propagation: a misfolded protein induces misfoldingProceedings of the National Academy of Sciences of the United States of America 102, 7835–40, 2005.
Structural genomics and its importance for gene function analysisNature Biotechnology 18, 283–287, 2000.
Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequencesThe Journal of Steroid Biochemistry and Molecular Biology 103, 357–60, 2007.
Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanismJournal of the American Chemical Society 133, 10283–9, 2011.
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transitionBiopolymers 69, 399–405, 2003.
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 fragment reconstruction using various modeling techniquesJournal of Computer-Aided Molecular Design 17, 725–38, 2003.
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecABiophysical journal 94, 2482–91, 2008.
On the origin of the cooperativity of protein folding: implications from model simulationsProteins 26, 271–287, 1996.
Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulationsProceedings of the National Academy of Sciences of the United States of America 95, 1020–1025, 1998.