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What is ProShape ?
It is widely believed that the geometry of a protein plays a crucial role
in its folding process as well as in its interactions with other bio-molecules
or small ligands, yet geometrical methods are still uncommon in computational
biology because several unresolved representational and algorithmic issues
remain. ProShape is designed to provide answers to some of these issues.
ProShape is an ongoing effort, whose aim is to develop new computational
techniques for simulating, analyzing and visualizing protein structures.
It will provide access to new software whose aim is to help structural
biologists with their research.
Different representations of the B1 immunoglobulin binding
domain of the streptococcal protein G
For simplicity, only the CA are shown
A) Cartoon of the backbone of the protein: strands are shown
in green, helices in red.
B) Corey-Pauling-Koltun or CPK or space filling representation:
each atom is represented as a ball.
C) The alpha-shape complex of the union of balls shown in B).
Our initial effort is focused on understanding the surface and volume
of the space filling diagram of a protein.
The Surface and Volume of Protein Structures
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Surface, Volume of Proteins and their Energetics
The accurate modeling of protein in solution using molecular mechanics
requires realistic models for the interaction of the solvent with the molecule.
To treat such a medium (usually water) in a molecular calculation, both
explicit and implicit solvent models have
been developed. While explicit models rely on using hundreds or thousands
of discrete solvent molecules, implicit solvent models treat the solvent
as a continuous medium having the average properties of the real solvent,
and surrounding the solute beginning at the van der Waals surface. Most
continuum models relate the energetics of the interaction of the solvent
with the protein to the geometry of this surface. A small review of implicit
solvent models is available here
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Computing Protein Surface and
Volume: an Overview
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ProGeom: a new program for computing Protein Surface,
Volume, and their Derivatives
We have developed a new method for computing the surface area and
volume of a protein, as well as their analytical derivatives with respect
to atomic positions. This method is based on the Alpha
Shape theory. It is implemented into a new program, called ProGeom,
which was designed to be fast, robust, and accurate. Special attention
is given to problems of numerical instabilities, degeneracies, and discontinuities
(for the area derivatives).
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Pocket: a new program for detecting Protein Pockets
Active sites of proteins are often found in structural pockets or
cavities. The Alpha
Shape theory provides an analytical method for detecting pockets in
proteins, an measuring their volume and surface. This method was implemented
in a new program, called Pocket.
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ProGeom and Pocket: a Tutorial
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Software download
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