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 ).