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5th Annual Linux Showcase & Conference — Abstract
Chimera: Affordable Desktop Molecular Modeling On Linux
Workstations
David Konerding, Conrad Huang, and Thomas Ferrin, University of California, San Francisco
Abstract
Molecular modeling is a well-established tool
used in a variety of scientific disciplines, including
pharmaceutical chemistry (the development
of new drugs) and bioinformatics (the application
of information theory to biological sequence
analysis) [1]. Molecular modeling is frequently
used for planning experiments, analyzing the results
of experiments, and for making predictions
in situations where technical limitations make experiments
difficult or impossible. Recently the
Linux/GNU operating system, running on inexpensive
desktop PCs using video cards with powerful
hardware graphics acceleration, has grown
very popular in molecular modeling due to its
low cost, low barrier to use, and compatibility
with existing UNIX workstations. The Computer
Graphics Lab at the University of California San
Francisco [2] is developing an advanced modeling
application, Chimera [4], to succeed its well-regarded
but aging application, MidasPlus [3].
Chimera is written in C++ and Python and emphasizes
programmable extensibility as its primary
feature. In recognition of the increasing interest
in Linux as a molecular modeling platform,
we undertook a port of Chimera to Linux. Porting
Chimera to Linux represented a number of challenges
which had to be overcome; we describe
the problems we faced and our solutions.
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