Bioinformatics protein structure analysis

Bioinformatic tools are of increasing importance for the characterization of flavoenzymes. This finding holds for protein sequence and protein structural analysis as well as for gaining insight into the reactivity of the flavin cofactor by combined quantum mechanical and molecular mechanical (QM/MM) simulations (12). 

PROTEIN STRUCTURE ANALYSIS USING BIOINFORMATICS 619 Sensitive Search 1D/2D/3P Compatibility,... 

Ausiello G, ViaA, Hekner-CitterichM (2005) Query3d a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics 4(Suppl 6) S5... 

David, G. (2005) Covell Linking tumor cell cytotoxicity to mechanism of drug action An integrated analysis of gene expression, small-molecule screening and structural databases. Proteins Structure, Function, and Bioinformatics, 59 (3), 403-433. 

Proteomics server of the Swiss institute of bioinformatics. Dedicated to analysis of protein sequences and structure, as well as 2-D SDS-PAGE. 

The computer has become an essential tool in biochemical research. A computer may be used for the routine jobs of word processing and data collection and analysis. In addition, if a computer is connected to the Internet, then it may be used for biochemical literature searching, accessing information about nucleic acid and protein sequences, predicting protein structure, and seeking research methodology. In this experiment, students will be introduced to all of these skills in bioinformatics. 

Sequence analysis is a core area of bioinformatics research. There are four basic levels of biological structure (Table 1), termed primary, secondary, tertiary, and quaternary structure. Primary structure refers to the representation of a linear, hetero-polymeric macromolecule as a string of monomeric units. For example, the primary structure of DNA is represented as a string of nucleotides (G, C, A, T). Secondary structure refers to the local three-dimensional shape in subsections of macromolecules. For example, the alpha- and beta-sheets in protein structures are examples of secondary structure. Tertiary structure refers to the overall three-dimensional shape of a macromolecule, as in the crystal structure of an entire protein. Finally, quaternary structure represents macromolecule interactions, such as the way different peptide chains dimerize into a single functional protein. 

Wishart, D., 2005, Protein structure and analysis. In Baxevanis, A.D. and Ouellette, B.F.F., (Eds), Bioinformatics A practical guide to the analysis of genes and proteins, 3rd Edition, Wiley-Interscience, 223-251. 

The terms bioinformatics and cheminformatics refer to the use of computational methods in the study of biology and chemistry. Information from DNA or protein sequences, protein structure, and chemical structure is used to build models of biochemical systems or models of the interaction of a biochemical system with a small molecule (e.g., a drug). There are mathematical and statistical methods for analysis, public databases, and literature associated with each of these disciplines. However, there is substantial value in considering the interaction between these areas and in building computational models that integrate data from both sources. In the most... 

Gradually, over the past twenty years, mass spectrometers were interfaced with a number of protein chemistry assays to generate detectors providing superior information. With the increased performance and versatility of the instrumentation dedicated to the life sciences, new analytical strategies for peptide and protein identification and characterization have emerged in which MS and bioinformatic tools are key players. MS has an enormous impact on the capability for structural analysis of bio-molecules, thanks to the ability to create gas phase ions of the peptides and proteins to be analyzed. Peptides and proteins are often charged and polar, making... 

Y. Mu, P. H. Nguyen, and G. Stock (2004) Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins Structure, Function, and Bioinformatics 58(1), pp. 45-52... 

For example, see E. N. Baker, V. L. Arcus and J. S. Lott. Protein structure prediction and analysis as a tool for functional genomics. Applied Bioinformatics,... 

---