What is ProShape ?

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

 
• 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
 

• Computing Protein Surface and Volume: an Overview

 

 

• 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).
 

• 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.
 
 

• ProGeom and Pocket: a Tutorial

 

 

• Software download