How is Cyrus different from other modeling software?
For over a half century, molecular modeling methods have been applied to small molecule discovery, with many notable successes. Focus is now increasingly being directed to proteins as therapeutics or synthetic biology tools, and to computational methods that can be applied to the structure prediction and design of these valuable proteins. Much of this protein comparative modeling and design work has been based solely on predictive approaches derived from first principle physics.
Rosetta, available commercially as Cyrus Bench, has fundamentally changed protein structure prediction and protein design through the use of a scoring function that reflects a combination of key physical insights from traditional methods and statistical knowledge from the vast accumulation of protein structures solved over the last six decades. This combined approach is very different from all other commercially-available software toolkits such as Schrodinger and CCG Moe, and has leapfrogged other methods for protein modeling.
This has lead to many “firsts” in the field of protein design, including the first fully software-designed proteins, the first designed proteins with biochemical characteristics as good as or better than a therapeutic antibody (protein interactions design) or enzyme, and the first designed proteins in human clinical trials (Tocagen and PVP Bio). Rosetta protein modeling software is broadly useful in protein folding simulation (protein structure prediction), protein structure analysis, protein visualization, and structural protein analysis and design.
These Rosetta tools are now accessible through Cyrus Bench, and are helping Cyrus customers advance their discovery programs into pre-clinical and clinical trials.
Foldit was created by Rosetta scientists to enable citizen science – it is a graphical version of Rosetta where scientist clients can submit a protein prediction problem to be solved by many users around the world. It is used in many Rosetta labs to gather new solutions to real scientific problems from citizen scientists around the world, and has solved key scientific problems including a protein structure from the simian immunodeficiency virus (SIV). Many scientific users outside of Rosetta labs have expressed a need for a tool like Foldit, but one where they can input their own proteins with all of their complex binding partners (small molecules, metal ions, nucleic acids, etc.) and carry out large scale Rosetta calculations. At the same time many scientists expressed a need for an easier to use version of Rosetta. Cyrus Bench was created to meet those needs for an easy to use Rosetta, or a more customizable and powerful version of Foldit, for biochemists and scientists to use on their own problems.
Our mission at Cyrus is to transform therapeutics and synthetic biology discovery, accelerating new treatments and protein-based materials to market, and creating entirely new treatments computationally that are difficult or impossible to identify using conventional means.
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