Vortex includes many capabilities that allow scientists engaged in biologics drug discovery and other biology research to easily analyze and visualize their data. Vortex intrinsically understands biological data types, including peptide and nucleotide sequences, antibody structure and features, and modified residues, simplifying the process of loading, viewing and analyzing sequence and structure data. Many standard bioinformatics analyses are integrated and simple to run directly from the graphical user interface, and advanced analyses such as Biological Sequence Activity Relationships (B-SAR) and Matched Pair Analysis (MPA) enhance scientific decision making to accelerate the progress of discovery projects.
Vortex for biologics discovery enables scientists to load sequence, structure, computational and experimental data from files or databases to create tables of live sequences and structures in Vortex. Sequence displays are interactive and the user can set a variety of display modes including linear and hyperbolic sequence views, and one- and three- letter residue codes.
Users can then apply standard bioinformatics analyses to their sequences, including alignment to a reference sequence, cross alignment amongst a set of sequences, and clustering. A variety of sequence alignment methods are included, and using built-in intelligence users can allow the software to automatically select the most appropriate algorithm based on the data. So, for example, different methods will be appropriate for the alignment of small sets of very short sequences, versus a cross comparison between very large sets of much longer sequences. As well as applying all the standard visualizations from Vortex, users can select visualizations appropriate to this kind of data such as CIRCOS plots and B-SAR plots.
Vortex for biologics discovery supports rich sequence annotation. Types of annotations includes text, regions, other sequences, small molecules (e.g., conjugates), and oligomers. Users can add annotations manually or apply library searches to identify regions within the sequences such as antibody complementarity determining regions (CDRs). Ontologies can be loaded and integrated with sequence data to provide comprehensive information for analyses. When activity data is loaded alongside biomolecular data, B-SAR analysis and visualization can be applied that relates that activity to the structure and/or sequence.
Vortex for biologics discovery is designed to be used by a wide variety of biologists, ranging from those primarily focused on laboratory work, to computational biologists, and expert bioinformaticians who can use the scripting capabilities of Vortex to define new methods or to integrate other third-party code, and then make these available to their wider Vortex user community.