William Humphrey

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VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each(More)
2 Summary NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design implemented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decomposition coupled with a multithreaded, message-driven design which is shown to(More)
The primary all-trans --> 13-cis photoisomerization of retinal in bacteriorhodopsin has been investigated by means of quantum chemical and combined classical/quantum mechanical simulations employing the density matrix evolution method. Ab initio calculations on an analog of a protonated Schiff base of retinal in vacuo reveal two excited states S1 and S2,(More)
The idiotype present on the Fab of a phosphorylcholine-binding IgA myeloma protein TEPC 15 (T15) of BALB/c origin was found in normal serum of BALB/c mice. Molecules carrying the T15 idiotype in normal serum could be adsorbed with Sepharose phosphorylcholine beads and R36A pneumococci. The T15 idiotype is absent in germ-free BALB/c but appears when the mice(More)
Exocytosis of cytolysin-containing granules from cytotoxic T lymphocytes (CTL) was studied with the use of granule enzyme (BLT esterase) as a convenient biochemical marker. Using cloned CTL, we demonstrate here that BLT esterase secretion into the supernatant is specifically triggered by antigen-bearing target cells and that this secretion is inhibited by(More)
MDScope is an integrated set of computational tools which function as an interactive visual computing environment for the simulation and study of biopolymers. This environment consists of three parts: (1) vmd, a molecular visualization program for interactive display of molecular systems; (2) namd, a molecular dynamics program designed for performance,(More)
The early stages of the bacteriorhodopsin photocycle, including the J625, K ~ w , and L550 intermediates and the role of water molecules within the protein interior, are studied by means of molecular dynamics simulations. Our calculations examine two models for the excited state potential surface governing the observed all-trans 13-cis photoisomerization:(More)