Data mining protein structure

Data-mining is the process by which testable hypotheses are generated regarding the function or structure of a gene or protein of interest by identifying similar sequences in better characterized organisms. For example, new insight into the... 

Liquids and proteins are complex systems for which the smdy of dynamical systems has wide applicability. In the conference, relaxation in liquids (s-entropy by Douglas at the National Institute of Standards and Technology, nonlinear optics by Saito, and energy bottlenecks by Shudo and Saito), energy redistribution in proteins (Leitner and Straub et al.), structural changes in proteins (Kidera at Yokohama City University), and a new formulation of the Nose-Hoover chain (Ezra at Cornell University) were discussed. Kidera s talk discussed time series analyses in molecular dynamics, and it is closely related to the problem of data mining. In the second part of the volume, we collect the contributions by Leitner and by Straub s group, and the one by Shudo and Saito in the third part. 

Ivanciuc, O., Schein, C.H. and Braun, W. (2002) Data mining of sequences and 3D structures of allergenic proteins. Bioinformatics, 18, 1358-1364. 

Structural (topological) Databases The structural databases play a central role in chemistiy because they contain information on chemical stmctures. Examples of this type are CAS registry, National Cancer Institute (NCI) database, Crystallographic Stracture Database (ICSD), CSD, Protein Data Bank (PDB), etc. The structure databases are usually designed to store chemical stmctinal information representing the chemical bonds and atoms in such a way to use them for computational operations, such as structure search, data mining, etc. 

Zheng, H., Chruscz, M., lasota, P., Lebioda, L., and Minor, W. (2008) Data mining of metal ion environments present in protein structures. Journal of Inorganic Biochemistry, 102, 1765-1776. 

The data reported in these manuscripts demonstrates the enz3rmatic s)mthesis of homo- and heteropolypeptides. Data mining has expanded both the diversity and chain length of the resultant polypeptides. Recently, the crystal structure YwfE has been reported which will assist in the development of protein design studies. Engineering the reaction media for enhanced solubility of the polypephdes may influence the molecular weight. 

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