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Minehardt, T J; Kollman, P A; Cooke, R et al. (2006) The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin. Biophys J 90:2445-9
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Wang, Junmei; Kang, Xinshan; Kuntz, Irwin D et al. (2005) Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. J Med Chem 48:2432-44
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Duan, Yong; Wu, Chun; Chowdhury, Shibasish et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999-2012
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Chong, Lillian T; Bandyopadhyay, Pradipta; Scanlan, Thomas S et al. (2003) Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. J Comput Chem 24:1371-7
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Naber, Nariman; Minehardt, Todd J; Rice, Sarah et al. (2003) Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules. Science 300:798-801
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Gouda, Hiroaki; Kuntz, Irwin D; Case, David A et al. (2003) Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers 68:16-34
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Masukawa, Kevin M; Kollman, Peter A; Kuntz, Irwin D (2003) Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. J Med Chem 46:5628-37
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Minehardt, Todd J; Marzari, Nicola; Cooke, Roger et al. (2002) A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP. Biophys J 82:660-75
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Massova, Irina; Kollman, Peter A (2002) pKa, MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step. J Comput Chem 23:1559-76
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Dixon, Richard W; Radmer, Randall J; Kuhn, Bernd et al. (2002) Theoretical and experimental studies of biotin analogues that bind almost as tightly to streptavidin as biotin. J Org Chem 67:1827-37
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