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Y. Zhou, H. Zhou, and M. Karplus, ``Cooperativity in Scapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water'', J. Mol. Biol., 326, 593--606 (2003).

A. Linhananta and Y. Zhou, ``The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Go model of fragment B of Staphylococcal protein A'', J. Chem. Phys., 117,
8983--8995 (2002).

H. Zhou and Y. Zhou, ``Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction'', Protein Science, 11, 2714--2726 (2002).

H. Zhou and Y. Zhou, ``The stability scale and atomic solvation parameters extracted from 1023 mutation experiments'', Proteins, 49, 483--492 (2002).

A. Linhananta, H. Zhou and Y. Zhou, ``The dual role of a loop with low loop contact distance in folding and domain swapping'', Protein Science, 11, 1695-1701 (2002).

H. Jang, C. K. Hall, and Y. Zhou ``Protein folding pathways and kinetics: Molecular dynamics simulations of beta-strand motifs'', Biophys. J. 83, 819-835 (2002).

Y. Zhou and A. Linhananta, ``Role of hydrophilic and hydrophobic contacts in folding of the second beta-hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model'', Proteins, 47, 154-162 (2002).

Y. Zhou and A. Linhananta, ``Thermodynamics of an all-atom off-lattice model of the fragment B of Staphylococcal protein A: Implication for the origin of the cooperativity of protein folding'', J. Phys. Chem. B, 106, 1481-1485 (2002).

H. Jang, C. K. Hall, and Y. Zhou ``Folding thermodynamics of model four-strand antiparallel beta-sheet proteins'', Biophys. J. 82, 646-659 (2002).

Y. Zhou, M. Karplus, K. D. Ball and R. S. Berry, ``The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and
homopolymers'',J. Chem. Phys., 116, 2323-2329 (2002).

H. Zhou and Y. Zhou, ``Folding rate prediction using total contact distance.'', Biophys. J. 82, 458--463 (2002).

Y. Zhou, ``Fast and accurate thermodynamics of square-well systems from umbrella-sampling simulations of hard-sphere systems.'', J. Chem. Phys. 115, 7550-7553 (2001).