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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.
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.
Computer simulations of protein folding with a small number of distance restraintsActa Biochimica Polonica 49, 683–692, 2002.
Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipperBiophysical Journal 83, 2801–2811, 2002.
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.
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.
Exploring protein energy landscapes with hierarchical clusteringInternational Journal of Quantum Chemistry 105, 826–830, 2005.
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of modelsProteins 61 Suppl. 7, 84–90, 2005.
A minimal proteinlike lattice model: an alpha-helix motifThe Journal of Chemical Physics 122, 214915, 2005.
Protein modeling with reduced representation: statistical potentials and protein folding mechanismActa Biochimica Polonica 52, 741–8, 2005.
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.
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.
Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained modelsBMC Structural Biology 8, 36, 2008.
Folding pathway of the b1 domain of protein G explored by multiscale modelingBiophysical Journal 94, 726–36, 2008.
Selection of optimal variants of Gō-like models of proteins through studies of stretching.Biophys J 95, 3174-91, 2008.