Computational Biochemistry and Biophysics

By O. Becker, Alexander D. MacKerell, Benoît Roux, Masakatsu Watanabe. 2001

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Theoretical and computational models of biological ion channels (2004, methodology): “It consists in constructing an atomic model of the macromolecular system, representing the microscopic forces with a potential function, and integrating Newton's classical equation ' F=MA ' to generate a trajectory (for a recent review of simulation methods, see chapters 1–4 in Becker et al. 2001).”
CHARMM‐GUI: A web‐based graphical user interface for CHARMM (2008, methodology): “org, or uploaded from user’s computer) into CHARMM readable files with the following options: (1) partial selection of protein chains as well as model selection in the case of NMR structures, (2) modification of engineered residues, (3) terminal group selection, (4) protonation selection, (5) disulf”
The Amber biomolecular simulation programs (2005, neutral): “5.”
Nonequilibrium work theorem for a system strongly coupled to a thermal environment (2004, background): “) To be absolutely precise, for any process during which the work parameter is varied from A to B, the quantity ∆F appearing in equation (1) is defined by (see equations (2), (21))”