William Humphrey

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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)
Modern computational structural biology requires scientists to employ a wide range of tools and techniques to solve complex problems while keeping accurate records of research activities. Additional complications are introduced by the need to effectively engage in interdisciplinary collaborations with geographically dispersed colleagues. The software(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)