Additional Filters and Major (Silent) Changes
We continue to deliver on our initiative to improve our platform’s underlying infrastructure this month, making substantial changes to our underlying database and its organization. As communicated last months, these mainly internal activities will support planned changes to the platform in the upcoming months to provide our users with improved overall performance. On top of these underlying improvements, our team has also included additional ways to filter results in the platform, including the ability to search Keywords and EC numbers. More on these enhancements below.
Filtering by Keywords
Keywords make it easier to filter the results generated by deep proteome screening. Keywords are a controlled vocabulary assigned to proteins and linked to UniProt. Cyclica’s filters allow you to search keywords directly within the LigandExpress platform. There are 10 categories within this single Keywords filter, which include: Biological process, Cellular component, Coding sequence diversity, Developmental stage, Disease, Domain, Ligand, Molecular function, Post-translational modification, and Technical terms. These Keywords can be combined with any other fitler in the system to quickly hone results to those which are relevant to your biological question.
Applying EC Numbers to the Putative List
Another convenient way to filter through results generated by proteome screening is using Enzyme Commission (EC) numbers. EC number is a classification system that groups proteins based on their enzymatic functions. EC numbers are hierarchical, with the number becoming increasingly more specific with the addition of each digit to the EC number. For example, receptor protein-tyrosine kinases have an EC number of 188.8.131.52; the number 2.7.10 corresponds to Protein-tyrosine kinases; 2.7 are proteins that transfer phosphorus-containing groups; EC number 2 are all transferases. Travel down different EC numbers to find the class that is most relevant to your biological system.
March has been a highly productive month with our team improving implementation of how our data is organized and accessed. This month, we expect to bring another innovation to the hands of our users, which will enable better selection of lead/drug compounds. Further, the changes to our database will allow us to build more ways for our users to interrogate results. Missed our other release notes? Read all of Cyclica’s product updates at https://cyclicarx.com/product.
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.
We are looking for some enthusiastic testers to help Cyclica refine its technology. If you are interested please contact email@example.com.