Informatic tools

Hitoshi dedicated his life to Science and to the organization of Science. As a scientist, I remember the studies by X-ray of the coordination compounds in solution of metal ions with monodentate ligands which constituted milestones in the field. Eventually, he started simulating through informatic tools the interaction of solvents and ligands with metal ions. 

Fig. 4. Application of bioinformatics tools to 2D-DIGE data analysis. Proteome data consisting of the normalized spot intensity values are exported from the image analysis software and their correlation with clinicopathological data examined. Using informatics tools including clustering algorithms and machine-learning methods, a novel cancer classification based on proteome data is established, and key proteomic features and proteins corresponding to biomarker candidates are identified.

Ekins S, Freundlich JS, Choi I (2011) Computational databases, pathway and chem-informatics tools for tuberculosis drug discovery. Trends Microbiol 19 65-74... 

In contrast, the emerging theme in knowledge based modelling is an ever closer intertwining of modelling and experimentation. A powerful combination of three factors contribute to this theme (i) structure-property relationships that are based on better models and more relevant structural descriptors (ii) robotics techniques in experimentation, which lead to a real explosion in the amount of data available (iii) informatics tools, which can handle the large amounts of data generated by both experiment and simulation. 

Informatics Tools for Glycomics Assisted Interpretation and Annotation of Mass Spectra... 

We now introduce a new informatics tool called Shape Signatures that shows promise for drug discovery and computational toxicology. In contrast to QSAR and other descriptor-based approaches that compute hundreds of discrete descriptors for each molecule, the Shape Signature can be viewed as a very compact descriptor that encodes molecular shape and electrostatics in a single entity [76-78]. 

Strand with the two strands being linked by the H-bonds represented in Figure 2.9 between the two sets of complementary bases. This was in 1953 a discovery that reveals an extraordinary intuition from Watson and Cricks, especially when one considers the techniques that were available at that period of time, in particular the absence of informatics tools. 

The applications are numerous, but the main challenge is to analyze the outcome and to use this massive databank to infer valuable biological information using mathematical and informatics tools. 

The widespread use of PCR amplification in microarray manufacture places much importance on the availability of informatics tools for automated primer design. A primer is a synthetic oligonucleotide that hybridizes to a complementary nucleic acid template, and expedites (primes) enzymatic synthesis by providing a starting point for enzyme. PCR primers bind to proximal and distal sites on cDNA templates, allowing target sequences... 

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