Breaking free from chemical spreadsheets

Practical Applications of Matched Series Analysis: Sar Transfer, Binding Mode Suggestion and Data Point Validation

“…As projects enter the later stages of optimisation, this analysis will enable the selection of the most useful compounds to synthesise, to improve activity, test a binding hypothesis or if a leading chemotype unexpectedly become unsuitable for further development. The network layout of the results as cards containing structural information [11] also makes visualisation of the results a facile process and large datasets (several thousands of compounds), typical of the size generated within a long running project, can be analysed very quickly with the Matsy/SAR transfer methodology.…”

“…An overview of the MSA output from the analysis of the PPAR data set is shown in Figure 3(a), where each compound in the output data set is represented by a card [11]. Links between cards indicate the matched series in the data set that, in turn, lead to the novel suggested derivatives, resulting in a network of cards that illustrate the relationships in the data set.…”

Progress in visual representations of chemical space

“…Scaffold Hunter suggests positioning compounds on the concentric circles, each of which represents the next level of functionalization of the central fragment, whereas Scaffold Explorer groups the compounds according to the scaffolds and constructs the trees by a sequential functionalization. A similar approach is realized in CardView module of StarDrop software suite [92,93], allowing a user to perform all required clusterings and groupings of the compounds based on his own expert knowledge, thus extending the possibilities of the formal silicon logic to the fuzzy human logic. In this approach, the directed edges, colored by the similarity or another pairwise measure, can represent the property optimization sequence in the course of a project or custom tree organization principle.…”

Integrating Everything: The Molecule Selection Toolkit, a System for Compound Prioritization in Drug Discovery

“…There seem to be very few packages that put it all together into one integrated system. One package that puts much of this all together is produced by Optibrium; the package is called StarDrop . This package has several strengths; it uses utility functions (therein called “scoring functions”) aggregated to an overall desirability.…”

“…One package that puts much of this all together is produced by Optibrium; the package is called StarDrop. 27 This package has several strengths; it uses utility functions (therein called "scoring functions") aggregated to an overall desirability. It has predictive modeling capabilities, and it has extremely good visualization features.…”