Structural annotation

Annotation can take one of two main forms - biological annotation, which is the assignment of specific biological properties to known active compounds, and chemical/structural annotation, which will be the only focus of this chapter. 

Greenwald R, Golub L. Biologic properties of nonantibiotic, chemicaUy modified tetracyclines (CMTs) a structured, annotated bibhography. Curr Med Chem 2001 8(3) 237 2. 

CE amol-fmol Separation, profiling Rapid separation, isomeric resolution, small sample volume Limited databases for CE, standards required for structural annotation, limited compatibility with MS... 

A reference database of chemical structures, annotated by therapeutic indication or mechanism of action. For the purpose of illustration, we used the MDL Drug Data Report (MDDR) (11) which contains 65,367 molecules organized in 249 sets (tee Note 1). 

For each set a and b from collections Ca and Cb, respectively, calculate rab(t.) as previously described using only the optimal threshold t. from the background model. Be sure to use the actual molecule structures annotated for each set. 

DSSP 3-state secondary structure annotation for protein structures http //www.cmbi.kun.nl/swift/dssp/ W. Kabsch, C. Sander (distributed via CMBI, NL, G. Vriend) [305]... 

To discover protein functional or structural sequence motifs, you could select proteins belonging to a given protein family based on sequence similarity, structure, annotation, or other means (23,37,38). You might further refine the selection to only include proteins from organisms with a particular feature, such as the ability to live in extreme environments (39). Another protein motif discovery application uses information from protein-protein interaction experiments. You can assemble a set of proteins that bind to a common host protein, to discover sequence motifs for the interacting domains. 

Typically, the first step in structural annotation is to search the query structure against other structures deposited in the PDB using tools such as DALI [185], VAST, SSM [186], CE [187], DEJAVU [188], or MATRAS [189], If the structure contains multiple structural domains, it is advisable to split the structure into separate coordinate files and submit each domain separately for structural comparison. Structural domains can be identified using tools that rely on geometric criteria and protein dynamics, such as Protein Domain Parser [190], Domain Parser [191], or Domain-Finder [192]. Alternatively, domain composition can be evaluated by comparison to... 

D-GENOMICS http //www.sbg.bio.ic.ac.uk/3dgenomics Proteome structural annotations... 

Cell Wall Navigator Structural annotation of gene families involved in cell wall generation (lignin biosynthesis excluded) bioweb.ucr.edu/ Cellwall/... 

Demonstrated the applications of the library for high-throughput lipid identification [7]. The group analyzed lipid extracts of the human plasma using a low-resolution mass spectrometer. Using LipidBlast, they structurally annotated a total of 264 lipids. The data set was cross-checked with manual peak annotations and data available from Lipid MAPS. Using accurate mass LC-MS/MS, they annotated a total of 523 lipid molecular species. A similar number of plasma lipids were obtained in comparison to those previously published [8, 9]. 

Figure 4.155 Structure Annotated Product Ion Spectrum (Mass Frontier).

Drawing-, text-, and structure-input tools are provided that enable easy generation of flow charts, textual annotations or labels, structures, or reaction schemes. It is also possible to select different representation styles for bond types, ring sizes, molecular orbitals, and reaction arrows. The structure diagrams can be verified according to free valences or atom labels. Properties such as molecular... 

D images, and a variety of links to other resources bibliographic citations), the data entries are annotated by RCSB (Research CoUaboratory for Structural Bioinformatics) with additional information. 

The genome projects produce an enormous amount of sequence data that needs to be annotated in terms of molecular structure and biological function. 

Scientific information—the contextual interpretation of experimental data—is published as free text. The same applies to the annotation of experimental results, genes, proteins, and compounds and the description of medical conditions. This clearly indicates that scientific information is not structured, which creates a major challenge for its reuse, management, and statistical analysis. This fact has largely been recognized, and much research... 

Identify and extract chemical compounds from the text, transform them into structures and ask an external application to compute their chemical properties and toxicology alerts, and annotate the documents with these results. The added information might then be used for further analysis of the data set. 

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