Biomatics Based Biomedical Imaging Systems

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A Brief Introduction to Protein Crystallography by Dave Lawson

Model building

This is the process where the electron density map is interpreted in terms of a set of atomic coordinates. This is more straightforward in the molecular replacement case because we already have a coordinate set to work with. In the case of isomorphous replacement we simply have the map. It is essentially a 3-dimensional jigsaw puzzle with the pieces being the amino acid residues. The normal procedure is to fit a protein backbone first then if the resolution permits, we insert the sequence. The amount of detail that is visible is dependent on the resolution and the quality of the phases. Shown below is a high resolution electron density map with atomic coordinates superposed. Often regions of high flexibility are not visible at all due to static disorder, where the structure varies from one molecule to the next within the crystal, or dynamic disorder, where the region is mobile within the crystal. The latter type of disorder is eradicated in cryogenic data collection.




http://www.jic.ac.uk/staff/david-lawson/xtallog/summary.htm



Protein structure representation with subsequent analysis of all features related with this particular structure is a main goal of all protein crystallography studies. The amount of all programs, tools and utilities for protein structure analysis is significantly greater than those available for protein crystallography itself. Usually it is almost impossible to quickly select the best tools for protein structure analysis. For our studies we've not only used a lot of different programs but even developed some of them. Our guide will help you to select the perfect tools for protein structure analysis and read simple manuals and step-by-step algorithm for achieving requested results. All our programs described here are distributed for free.

http://proteincrystallography.org/

Fractal Procedures

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