Fingerprint motifs

As all mutation sites chosen in this study are limited to the (lap fingerprint motif, the strategy applied is applicable to other NAD+- and NADP+-dependent dehydrogenases. Indeed, a systematic replacement of amino acid residues in the Pap fingerprint motif in the NAD+-dependent dihydrolipoamide dehydrogenase from E. coli converted its cofactor specificity from NAD+ to NADP+14IL A similar strategy... 

As illustrated in the next section, the use of biological fingerprints, such as from a BioPrint profile, provides a way to characterize, differentiate and cluster compounds that is more relevant in terms ofthe biological activity of the compounds. The data also show that different in silico descriptors based on the chemical structure can produce quite different results. Thus, the selection of the in silico descriptor to be used, which can range from structural fragments (e.g. MACCS keys), through structural motifs (Daylight keys) to pharmacophore/shape keys (based on both the 2D structure via connectivity and from actual 3D conformations), is very important and some form of validation for the problem at hand should be performed. 

The site mainly offers useful software for sequence alignment such as ALIGN. It also offers some other useful tools such as PRINTS (Protein motif fingerprint data) and MAXD for microarray data storage and analysis. 

The sequence motifs identified in this way may be different from the motifs/ fingerprints listed in the Prosite [31], Blocks [75], and especially PRINTS [33, 76] databases, which use single or multiple conserved regions as consensus signatures to describe families or subfamilies and which are used as automated diagnostic tools for inserting new members into the framework of the already classified members. 

Figure 5.32. Some structurally diverse RGD antagonists matched through virtual screening using the RGD motif and 3D pharmacophore fingerprints.

The list of all motifs found in a crystal constitutes the first-level or unitary graph set of that crystal, and is a sort of fingerprint of a crystal that can help to distinguish between different polymorphs of the same crystal (for instance Form 2 of the iminodiacetic acid crystal contains six motifs and its first-level graph set is Ni = DDC(5)C(5)C(8)C(8), while Form 1 has only three motifs and its first-level graph set is Ni = C(5)C(8)R2(10). 

Vibrational spectroscopy is a powerful tool for the study of molecular structure and dynamics. The typical vibrational frequency range of this spectroscopy is 100-4000 cm, which corresponds to the energy range 0.3-12 kcal/mol. Because the resolution of vibrational spectroscopy is on the order of 5 cm , the band shift on this order corresponds to a 0.02 kcal/mol. Vibrational transitions are correlated with specific vibrational motions by inspection of the transition frequencies. From identification of these fingerprint vibrational modes, conclusions can be drawn on specific structural motifs in the molecules. Vibrational transitions have bandwidths typically smaller (10-20 cm ) than those from electronic transitions (typically 200-2000 cm ), and it is thus less probable that different transition bands overlap in vibrational spectroscopy than in electronic spectroscopy. In addition, small molecular species may always be probed through their vibrations, and electronic transitions. Major disadvantages of vibrational spectroscopy, on the other hand, are the inherent lower cross sections of vibrational transitions and the frequent overlap of the absorption bands with those of the solvent [10]. 

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