The development of BioCoRE is based on successful efforts in advanced software, novel algorithms and state-of-the-art hardware. The software developed is freely available to the biomedical community and is widely distributed. We have taken a broad approach, reflected in the modeling package MDScope ( Nelson et al., 1995 ) which includes our popular molecular graphics program VMD ( Humphrey et al., 1996 ).
Efforts have also been invested to apply parallel computer architectures for molecular dynamics simulations. To this end the program NAMD ( Nelson et al., 1996 ; Kalé et al., 1997 ; Kale et al., 1998 ; Kalé et al., n.d. ) has been developed. NAMD includes state-of-the-art algorithms, which are applicable in both serial and parallel computing environments. NAMD has been designed as a flexible program, incorporating many options to control integration methods, force field parameters, etc. It is user friendly and is easy to modify and extend to serve goals we have not foreseen ( Phillips et al., n.d. ). This modifiability is accomplished in NAMD through extensive user and programmer documentation, and free availability of source code written with an object-oriented design. NAMD is unique in the extent to which other researchers can transform it to perform specific tasks.
VMD is a mature visualization environment for structural biology. Many research groups have adopted VMD for plain visualization, docking studies, structure refinement, trajectory analysis, and interactive simulations ( Leech et al., 1996 ). Other capabilities include enhanced flexibility in display options, extensions to the scripting language, static docking, and structure alignment. Through the enhanced Tcl-based scripting language, new analysis routines may now be written by end-users without recompilation of VMD. The scripting language allows nearly all mouse actions to be logged to a script file, edited, and replayed, making it easy to produce on-line tutorials or high-quality movies. Synchronous VMD sessions on two workstations have already been achieved. VMD is web-aware and can function as a helper application for web tools.
BioCoRE is described from two perspectives in the following sections. Section illustrates BioCoRE from the user's perspective, whereas section presents the architecture of BioCoRE from the perspective of developers and implementors. For concreteness, the locally developed programs NAMD and VMD are assumed to represent the molecular graphics and dynamics components of BioCoRE although we intend to encompass other programs, e.g., RASMOL ( Sayle and Milner-White, 1995 ) or X-PLOR ( Brünger, 1996 ).