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For the past three years our group
has been developing ProteinShop, a visual infrastructure for the prediction
of the structure of proteins of realistic size and complexity. ProteinShop
was designed to bring interactive computing graphics into the field of
protein structure prediction to a level not attempted by other visualization
tools. It was motivated by our conviction that only such level of interaction
will help scientists simulate the folding, behavior, and interactions of
molecules on computers, learn about the complex biological systems at hand,
and ultimately accelerate time to solution. ProteinShop's initial goal was
to streamline and simplify the process of creating a variety of protein
structures by manipulating the proteins as if we could grab them with our
own hands, using an energy function to guide the process.
These configurations can be used as starting points to a
global
optimization algorithm. Although ProteinShop does not perform the
global
optimization process itself, it provides a framework that can be used
to
interact with a global optimization process that may be running on a
remote
machine.
ProteinShop was developed at the Lawrence Berkeley National Laboratory by researchers from Lawrence Berkeley National Laboratory, University of California at Davis, and Lawrence Livermore National Laboratory.
ProteinShop supports several advanced manipulation styles: interactive manipulation using an inverse kinematics algorithm, Ramachandran plots, alignment guides, global beta-sheet adjustments, and automatic beta-sheet formation. Each manipulation style is tailored to achieve very specific types of results. These styles constitute one of ProteinShop's primary contributions.
ProteinShop v3.0
under GPL
