Publications
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Protein modeling with reduced representation: statistical potentials and protein folding mechanismActa Biochimica Polonica 52, 741–8, 2005.
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamicsBiophysical Journal 99, 3507–16, 2010.
Protein structure prediction by tempering spatial constraintsJournal of Computer-Aided Molecular Design 19, 603–8, 2005.
T-Pile–a package for thermodynamic calculations for biomoleculesBioinformatics (Oxford, England) 23, 1840–1842, 2007.
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genomeProceedings of the National Academy of Sciences of the United States of America 99, 5993–5998, 2002.
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.
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.
Denatured proteins and early folding intermediates simulated in a reduced conformational spaceActa Biochimica Polonica 53, 131–143, 2006.
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transitionBiopolymers 69, 399–405, 2003.
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced modelBiophysical Journal 85, 3271–3278, 2003.
Does reptation describe the dynamics of entangled, finite length polymer systems? A model simulationThe Journal of Chemical Physics 86, 1567–1585, 1987.
Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of beta-barrel proteinsBiopolymers 26, 937–62, 1987.
Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptidesJournal of Chemical Physics 97, 9412–9426, 1992.
Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. II. Probe polymer in a matrix of different degrees of polymerizationThe Journal of Chemical Physics 86, 7174–7180, 1987.
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniquesBiophysical Journal 77, 2942–52, 1999.
Monte Carlo simulations of protein folding. I. Lattice model and interaction schemeProteins 18, 338-52, 1994.
The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model systemThe Journal of Chemical Physics 85, 3585–3597, 1986.
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo modelProteins 32, 475–494, 1998.
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of modelsProteins 61 Suppl. 7, 84–90, 2005.
Monte Carlo study of dynamics of the multichain polymer system on the tetrahedral latticeThe Journal of Chemical Physics 79, 1523-1526, 1983.
Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric meltThe Journal of Chemical Physics 86, 7164–7174, 1987.
Collapse transitions in protein-like lattice polymers: The effect of sequence patternsBiopolymers 42, 537–548, 1997.