Enhancing Ligand Express® with the MatchMaker™ Engine
In our previous Release Highlights we hinted towards significant changes coming to Ligand Express®. You may have seen our announcement of our enhanced predictive engine called MatchMaker™ to kick off the new year. MatchMaker allows us to more accurately and rapidly assess potential protein-ligand interactions. MatchMaker is powering Cyclica’s paradigm shift towards a holistic view of all proteins so we can design drugs for patients, not just a single protein. Given the market demand, we put aside our original release plans and focused exclusively on integrating the MatchMaker engine this month. With all available hands helping with the effort, we our pleased to announce that our team has successfully integrated the MatchMaker engine into Ligand Express. MatchMaker is the first technology in a wave of innovations that Cyclica has planned for Ligand Express in 2019.
Read on below for more information about MatchMaker integration and how you can start using it today!
What is MatchMaker?
MatchMaker is Cyclica’s newest innovation for predicting protein-ligand interactions at the proteome scale. In silico proteome screening was a fundamental challenge that Cyclica tackled with our first Ligand Express offering. Ligand Express revealed a drug’s polypharmacology allowing scientists to design better and safer medicines. While our best in class technology made understanding polypharmacology possible, we were aware of its limitations. We took the lessons we learned building our first generation Proteome Screening technology straight into our development of MatchMaker, a deep learning method that demonstrates dramatically increased accuracy, speed, and throughput compared to our Generation 1 approach. MatchMaker is trained on millions of known drug-target interactions combined with biophysical information from the protein’s sequence and 3D structure. Our benchmarking study revealed MatchMaker’s generalizability; it produced accurate results on previously unseen molecules and proteins. Further, its accuracy and throughput makes it comparable to in vitro proteome profiling technologies. With MatchMaker now powering Ligand Express, it is possible to rapidly assess hundreds to thousands of molecules and answer questions about target-of-action, toxicity, and efficacy faster than ever before.
Beyond these improvements, MatchMaker also expands our coverage within the human proteome enabling discovery in a wider range of disease relevant targets. Importantly, MatchMaker also removes our reliance on classical molecular docking to score and rank protein interactions, an approach that we acknowledge has several shortcomings. Perhaps the most exciting aspect of the MatchMaker engine is that its orders of magnitude performance enhancement supports further planned innovations at Cyclica. We look forward to sharing more about these innovations in the future.
How Can I Benefit from the MatchMaker Engine?
In this first phase of integration, the MatchMaker Engine will be bolsterings our previously released Proteome Screening technology. As long as you have access to Ligand Express, you will be able to use MatchMaker to uncover your small molecule’s polypharmacology (Please reach out to us at email@example.com if you would like to learn how you can access the technology). The results generated by MatchMaker will be navigable through the Ligand Express platform, allowing you to filter and explore data just like the Generation 1 technology. Results generated by our MatchMaker-enhanced software will be available up to 20 times faster, and we won’t be stopping there, with even more substantial speed boosts planned for future releases. With increased speed, throughput and accuracy, expect to see some changes to the look and feel of Ligand Express as we modify the platform to ensure that MatchMaker Proteome Screening will be utilized to its fullest.
While MatchMaker integration was taking place, our team was also hard at work putting together an improved queuing system for requests that require some additional processing power. This will allow for more seamless experience within the platform, and will facilitate new functionality in the future. This new system can be experienced first hand when downloading the ranked list of putative binders and all its associated information. Previously, the system paused while the download was being processed. With the new system, users can continue to use the platform while downloads are prepared and downloaded automatically.
We have also expanded our support of Firefox, with all major features supported by the browser. We are committed to testing on Firefox during every release cycle.
MatchMaker is the first of many innovations we plan on incorporating into Ligand Express. One major addition includes making our ADMET-P toolkit available on Ligand Express. Other plans include increased throughput and speed of MatchMaker-powered Proteome Screening, and necessary changes to the UI to facilitate this increase throughput. As we pave the way for these innovations there may be some releases where users see few changes in the UI, but that means some major innovations are on the horizon. We look forward to touching base next month to reveal new functionality within the platform.
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.