August 22, 2010

Status of Protein Structure Prediction and an Overview of Whole Proteome Analysis

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CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994.

The status of the protein structure field from 2008 is as follows:
Based on well- established measures, there was no essential progress in (protein folding prediction) modeling methods from CASP7 to CASP8 (2006 to 2008). In particular, the GDT_TS and alignment accuracy AL0 scores for the best models in general remain approximately at the same level, as they were 2 years ago. Although it is possible to tease out signs of progress, there is no doubt that overall recent CASPs have seen much smaller increments than earlier ones. In the past, we have seen bursts of progress from particular technical advances such as multiple sequence alignment methods, and fragment assembly procedures. Clearly, new methods are needed to push the field forward once again.

Wikipedia describes the methods used for protein structure prediction

Technologies for Whole Proteome Analysis (2005)

The information content of the genome is relatively static, but the processes by which families of proteins are produced and molecular machines are assembled for specific purposes are amazingly dynamic, intricate, and adaptive. All proteins encoded in the genome make up an organism's "proteome."
Proteins are molecules that carry out the cell's core work; they catalyze biochemical reactions, recognize and bind other molecules, undergo conformational changes that control cellular processes, and serve as important structural elements within cells. The cell does not generate all these proteins at once but rather the particular set required to produce the functionality dictated at that time by environmental cues and the organism's life strategy. A set of proteins is produced just in time and regulated precisely both spatially and temporally to carry out a specific process or phase of cellular development.

Understanding a microbe's protein-expression profile under various environmental conditions will serve as a basis for identifying individual protein function and will provide the first step toward understanding the complex network of processes conducted by a microbe. Insight into a microbe's expression profile is derived from global analysis of mRNA, protein, and metabolite and other molecular abundance. Characterizing a microbe's expressed protein collection is important in deciphering the function of proteins and molecular machines and the principles and processes by which the genome regulates machine assembly and function and the resultant cellular function. This is not a trivial feat. A microbe typically expresses hundreds of distinct proteins at a time, and the abundance of individual proteins may differ by a factor of a million. Technologies emerging only recently have the potential to measure successfully all proteins across this broad dynamic range.

DOE Strategic Plan for genomic science 2008

Here is a link to the DOE Strategic plan for genomic science and systems biology from 2008.

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