Publications
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo modelProteins 32, 475–494, 1998.
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.
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamicsBiophysical Journal 99, 3507–16, 2010.
Derivation of protein-specific pair potentials based on weak sequence fragment similarityProteins: Structure, Function, Bioinformatics 38, 3–16, 2000.
Does a backwardly read protein sequence have a unique native state?Protein Engineering 9, 5–14, 1996.
Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignmentsJournal of Molecular Biology 277, 419–448, 1998.
Folding pathway of the b1 domain of protein G explored by multiscale modelingBiophysical Journal 94, 726–36, 2008.
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of modelsProteins 61 Suppl. 7, 84–90, 2005.
Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization stepProceedings of the National Academy of Sciences of the United States of America 108, 9443–8, 2011.
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.
MONSSTER: a method for folding globular proteins with a small number of distance restraintsJournal of Molecular Biology 265, 217–241, 1997.
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.
Protein modeling and structure prediction with a reduced representationActa Biochimica Polonica 51, 349–71, 2004.
Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanismJournal of the American Chemical Society 133, 10283–9, 2011.
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.
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.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force fieldBMC Structural Biology 7, 43, 2007.
Why do proteins divide into domains? Insights from lattice model simulationsBiomacromolecules 8, 3519–24, 2007.