More Ways to Explore and Refine your Data
Happy Holidays! Cyclica has had a wonderful year, making significant strides towards revolutionizing drug discovery by bringing to the market the first end-to-end enabling cloud-based and AI-augmented platform that enhances how scientists design, screen, and personalize medicines, all with a polypharmacology twist. We have a bold vision, and we are driven, committed, and focused on building something remarkable by doing more with AI. Ultimately, we want to bring the best drugs to patients faster and at a lower cost to pharma.
With that in mind, Cyclica is living up to the spirit of the season by bringing an exciting variety of new features to our users. The newly implemented Variants table coupled with our ‘Protein Abundance’ filter allows our users to gain more biological insight than ever before. Along with these exploratory tools, we have also introduce some general improvements to our compound submission, including the ability to bypass Cyclica’s energy minimization engine. We also enhanced our UI, which includes a navigation sidebar in analysis view.
Continue reading for details on each of these changes!
Single Nucleotide Variant Table
Cyclica is on a journey to develop a technology that spans the drug discovery process, and we took a major step forward by including Single Nucleotide Variants (SNV) into the platform. SNVs, which include both polymorphisms and mutations for human proteins, can be found within the protein viewer. To access the SNV table, simply click on the “Variants” to open up the table. SNVs are ordered according to their impact on protein function or deleteriousness. By exploring variants of proteins, drug discovery researchers can be alerted to possible personalized medicine opportunties.
Users will be able to search through SNVs and find those linked to certain diseases, or to find those linked to a particular chromosome. Other searches include allele frequency and potential for deleteriously affecting protein function. Both allele frequency and deleterious scores are calculated using multiple protocols, which are available as additional columns within the interface. This is our first step towards driving computational insights to support personalized medicine.
Bypass Energy Minimization
Our system accepts 2D or 3D representations of small molecule structures. In the case of 2D representations, Cyclica generates energy minimized 3D conformers to run through Ligand Express. Previously, 3D molecule also went through the energy conformer sampling process as well. Moving forward, it is now possible to override Cyclica’s Energy Minimization when submitting 3D structures that have already undergone energy minimization. This can easily be done during the submission process by de-selecting the “Minimize Structure” checkbox.
Change is good! The ability to switch between the protein viewer and network analysis has moved into our sidebar. While not the most thrilling of changes to Ligand Express, the sidebar paves the way for some significant improvements coming to Ligand Express. And for our established users, we still have Network Graphs, we just changed where you can access them.
Filter by Protein Abundance
Experimentalists work within model systems, which are derived from particular tissue or cell types. Knowing the biological context when exploring within Ligand Express helps interpret proteome screening results. By enabling users to filter results based on whether or not that protein is found within a given tissue or cell type, Scientists can help refine results to those most relevant to experimental observations. Simply click on “Tissue” within the filter drop down, select your tissue, and click go to see a list containing only proteins found within that specific cell or tissue type.
Cyclica is gearing up for some significant changes in the New Year. We’re not yet ready to release details as we are finalizing our validation work and documentation, but we believe it will radically change the way our users will interact with our technology. We are working hard throughout the holidays to bring these changes to our platform and into the hands of our users as soon as possible. I can’t wait to tell you all about it!
Are you a fan of the changes made to Ligand Express? All feedback is greatly appreciated! We would love to hear from you, please send any feedback to firstname.lastname@example.org.