Biologics: Bigger and better tools

Recognising the increased importance of Biologics in modern drug discovery, DesertSci has been developing a range of new tools for analysing structural features of biologics.  These have now been added to the Proasis suite.

We have incorporated methods for the comprehensive automated annotation of CDRs in antibody heavy and light chains, as well as tools for searching, retrieving, extracting, overlaying, and clustering of CDRs.

DesertSci uses powerful pattern matching software that allows for the fine-grained control of the number of aminoacid substitutions, insertions, and deletions in any CDR.

Overlays of matching CDRs is then available with the click of the mouse.

Clustering of matching can be done using affinity propagation, which is best described by the authors Frey and Dueck [1] as an “algorithm that identifies exemplars among data points and forms clusters of data points around these exemplars. It operates by simultaneously considering all data point as potential exemplars and exchanging messages between data points until a good set of exemplars and clusters emerges.” This method has been found to work very well for CDR motifs [2], giving Proasis users better and more effective insights for the design of new antibodies.

[1] J. Frey and D. Dueck. Clustering by passing messages between data points. Science, 2007, 315(5814)

[2] B. North, A. Lehmann, R.L. Dunbrack Jr., A new clustering of antibody CDR loop conformations. J. Mol. Biol. 2011, 406(2)