Cyrus Biotechnology featured in BIOCENTURY article on de novo Protein Design Revolution

SEATTLE, WA July 29, 2019 — Cyrus Biotechnology, Inc., a Seattle-based biotech software company commercializing Rosetta, the most advanced computational protein design platform, has been mentioned in the BIOCENTURY’s article:

Institute for Protein Design’s de novo revolutionHow a Seattle hub is overhauling protein- and cell-based therapies by breaking free o evolution’s constraints.

The BIOCENTURY article can be found here.

About Cyrus Biotechnology
Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering Cyrus Bench®, a SaaS platform for protein engineering to accelerate discovery of biologics and small molecules for the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus Bench® is based on the Rosetta software from Prof. David Baker’s laboratory at the University of Washington, the most powerful protein engineering software available. Cyrus customers include 12 of the top 20 Global Pharmaceutical firms and is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, and W Fund.

https://cyrusbio.com/

Cyrus Biotechnology Protein Engineering Scientist Amanda Duran to Speak at Precision Medicine & Ion Channel Retreat 2019

SEATTLE, WA July 26, 2019 — Cyrus Biotechnology, Inc., a Seattle-based biotech software company commercializing Rosetta, the most advanced computational protein design platform, announced today that Dr Amanda Duran, Cyrus Bio Protein Engineering Scientist, will speak at the Precision Medicine & Ion Channel Retreat in Vancouver, British Columbia, Canada.

DETAILS:

Title: Functional and Mutational Analysis with Rosetta and Cyrus Bench: KCNQ1 case study

Date: Friday, July 26th, 2019

Time: 2:40 PM PDT

Venue: Sheraton Vancouver Wall Centre

PMICR 2019 Program

http://www.aurorabiomed.com/wp-content/uploads/2019/07/Final-2019-Program-1.pdf

ABSTRACT:

Ion channels are one of the largest drug targets likely due to their role in regulation and signal transduction. KCNQ1 is a voltage-gated potassium channel associated with cardiac arrhythmias such as Long-QT syndrome. Several structures of the voltage sensing domain (VSD) or the pore domain have been resolved; however, there are no known structures of a resting VSD. In order to understand the mutational effects, the inactive VSD, closed pore state of KCNQ1 was modeled using Rosetta. RosettaCM enables the use of multiple templates in addition to fragment insertion during homology modeling. Knowledge from experimental studies of the charged residue pairing placement in the VSD was used as a filter during model selection. Finally, MolProbity, ProCheck, and PoreWalker were used to further assess the quality of the selected models.

Several methods exist for modeling mutation-induced stability changes from proteins of known structure or homology models; however, many of these methods perform poorly for membrane proteins. The amount of mutant thermostability data that is available for membrane proteins is sparse, making it nearly impossible to train an accurate predictor for the stabilizing effects of mutations. In a membrane protein benchmark, Rosetta outperformed most of the 10 methods assessed and was able to correctly classify nearly 70% of mutations as destabilizing. Combining these modeling efforts may help with identifying disease-associated mutations in the future. Cyrus Bench is capable of rapidly assessing the stabilizing effects of single point mutations using the newest Rosetta scoring function and thoroughly benchmarked protocols.

For more information on Cyrus Bench, click here.

About PMICR 2019
Over the last 16 years, the Precision Medicine and Ion Channel Retreat (PMICR) has evolved into one of the premier conferences for drug discovery, genomics and ion channel research. The 17th annual PMICR strives to continue this proud tradition by providing a platform to explore cutting edge technology and innovative research from around the world. This diverse, thought-provoking event allows academic and industry researchers to share knowledge, exchange ideas and establish fruitful partnerships. The Retreat is designed to maximize networking opportunities, with social events providing an intimate & relaxed atmosphere.

http://www.aurorabiomed.com/precision-medicine-ion-channel-retreat-2019/

About Cyrus Biotechnology
Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering Cyrus Bench®, a SaaS platform for protein engineering to accelerate discovery of biologics and small molecules for the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus Bench® is based on the Rosetta software from Prof. David Baker’s laboratory at the University of Washington, the most powerful protein engineering software available. Cyrus customers include 12 of the top 20 Global Pharmaceutical firms and is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, and W Fund.

https://cyrusbio.com

Cyrus Biotechnology Integrates DNA/RNA Support into its Rosetta-based Protein Design Platform

SEATTLE, WA May 29, 2019 — Cyrus Biotechnology, Inc., a Seattle-based biotech software company commercializing Rosetta, the most advanced computational protein design platform, is announcing the release of novel software capabilities to handle protein interactions with DNA & RNA as part of its Cyrus Bench® platform.

“Proteins that interact directly with DNA and RNA are part of an increasing number of early discovery pipelines across the BioPharmaceutical industry, ranging from CRISPR proteins to enzymes for DNA synthesis and modification,” notes Cyrus CEO Dr. Lucas Nivon. “At Cyrus we can now accelerate discovery in these key new markets with the newly released DNA/RNA Rosetta protein design capabilities in Cyrus Bench.”

Rosetta software is the world leader in protein modeling and design, with features including homology modeling and design to improve both protein affinity and protein stability. Rosetta combines both physical and statistical/machine learning methods, and differs from all other commercially available modeling software in the breadth of both application and experimental validation. Proteins designed using Rosetta are in pre-clinical or clinical evaluation by companies such as Tocagen, PvP Bio, Sana and Lyell.

These new features in Cyrus Bench® enable accelerated optimization and design of both tool compounds and therapeutic candidates, including polymerases, transcription factors, DNA modifying enzymes (e.g. CRISPRs), RNA modifying enzymes (e.g. isomerases) and other valuable compounds. These targets are critical to such fields as Therapeutics, Diagnostics, Agricultural Biotechnology and Biotechnology Tools.

These new software capabilities are available now to subscribers to Cyrus Bench® and to new customers who subscribe to the Cyrus Bench® suite of tools.

https://www.businesswire.com/news/home/20190529005228/en/Cyrus-Biotechnology-Integrates-DNARNA-Support-Rosetta-based-Protein

 

About Cyrus

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering Cyrus Bench®, a SaaS platform for protein engineering to accelerate discovery of biologics and small molecules for the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus Bench® is based on the Rosetta software from Prof. David Baker’s laboratory at the University of Washington, the most powerful protein engineering software available. Cyrus customers include 10 of the top 20 Global Pharmaceutical firms and is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, and W Fund.

https://cyrusbio.com/

 

Cyrus Contact – Lucas Nivon

lucas@cyrusbio.com

206-258-6561

 

Happy April 1! Announcing Cyrus ROSVAC-4!

Seattle, WA, April 1 2019. Cyrus Biotechnology is proud to announce a major step forward in computer biochemistry, the ROSVAC-4, an industrial-strength minicomputer custom-designed for simulations of biological molecules, with an astonishingly small 1900 sq ft. footprint, capable of over 10 simultaneous protein amino acid sequence calculations per annum, improving on ROSVAC-2 at 5 calculations per annum.
UNIVAC-I1951
Data is input into ROSVAC-4 using our proprietary PROTTAPES, custom-designed tape input and storage appliances capable of over 100 bytes per second data storage, recording an atomic protein structure in mere hours! ROSVAC-4 displays protein cartoon structures in beautiful 128×128 black and white pixels (ROSVAC-4 operator control booth pictured below). ROSVAC-4 requires a minimal staff of 5 technicians and 3 data entry staff, along with 1 glassblower and a part-time blacksmith for routine repairs.
Univac_w_prot
“The best part is how easy it is to use! I just startup the generator, rebuild the broken vacuum tubes, initiate startup procedures, finalize boot loading, set switches 7 through 1028 and then press the red button and turn the key” said ROSVAC-4 beta tester Steve Smith of the USAF. “Three months later I have results I can use.”.
“Why run on the cloud when you can have a ROSVAC-4 installed on-site in a dedicated room for only a few million bucks?”, says user John Jacobs at General Electric, “last time I checked its not raining!”.
Cyrus is taking orders for ROSVAC-4 now! Installation at your facility complete in 12-18 months. Prices start at only $15 million, and support contracts are available. Cyrus is also offering a 6 month training course at ROS-U for corporate technicians.
Thanks for reading! If it is not already clear, Cyrus is not really launching a ROSVAC-4, but we offer a best-in-class cloud-based protein modeling and design tool, Cyrus Bench based on Rosetta, with a set of new features released over the end of 2018 and early 2019 including arbitrary small molecule modeling (for small molecule discovery, e.g. more accurate modeling of drug/protein interactions) and antibody structure prediction. Learn more at our web site or Contact us at info@cyrusbio.com if you would like to watch a demo or get a quote.

Cyrus Biotechnology Exhibits at the PEGS Protein Engineering Summit in Boston, April 8th – 11th

March 26, 2019

SEATTLE, March 26, 2019 — Cyrus Biotechnology, Inc., a biotechnology software company offering advanced protein modeling and design tools to the Biopharmaceutical, Synthetic Biology, Chemical, and Consumer Products industries is pleased to announce its participation in the 15th Annual PEGS Boston Protein Engineering Summit in Boston, from April 8th through April 11th.

Dr. David Pearlman, Senior Fellow and Director of Customer Experience at Cyrus Bio, and Rosario Caltabiano, Executive VP of Sales, will attend the conference and discuss the latest advances in in silico protein engineering at booth 539 in the Boston Seaport World Trade Center Exhibit Hall.

Cyrus Biotechnology offers commercial tools based on the well-known Rosetta protein design package. The company is a spin out of David Baker’s laboratory at the University of Washington, established to make these tools easier to deploy and use. Cyrus has implemented the Rosetta platform with an easy to use interface on a computing cloud, resulting in high reliability software with high performance, usability and security. Cyrus Bench® software, and the underlying Rosetta software package, are already leveraged by many global pharmaceutical organizations, and Cyrus customers can apply the most advanced and validated in silico protein engineering science through an intuitive user interface for:

  • Protein Structure Prediction (best overall performance at CASP and CAMEO)
  • Antibody Structure Prediction from Sequence
  • Protein Stabilization
  • Computational Affinity Maturation (Interface Design)
  • Fast Free Energy Calculations
  • Prediction of Immunogenic Epitopes
  • Removal of Identified Liabilities
  • Protein Structure Optimization and Design
  • Antibody Engineering
  • Antigen Design
  • Enzyme Design and optimization

About Cyrus Biotechnology Inc.

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering Cyrus Bench®, a Software-as-a-Service (SaaS) platform for protein modeling and design capabilities to accelerate discovery of biologics and small molecules for the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus Bench® is based on the Rosetta software from the laboratory of Prof. David Baker at the University of Washington, the most powerful protein engineering software available. Cyrus customers include 10 of the top 20 Global Pharmaceutical firms and is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, and W Fund.

Cyrus Biotechnology Chief Science Officer Yifan Song to Speak at BAGIM – Boston Area Group for Informatics and Modeling

SEATTLE, WA March 11, 2019 — Cyrus Biotechnology, Inc., a Seattle-based biotech software company commercializing the advanced protein design platform Rosetta announced today that Dr Yifan Song, Cyrus Bio Chief Scientific Officer, will speak at an upcoming meeting of the Boston Area Group for Informatics and Modeling (BAGIM).

Topic: Got Structure? State-of-the-art protein structure prediction with homology modeling

Date: Thursday, March 14th, 2019

Time: 6:00 PM EDT

Venue: Shire – 125 Binney St, Cambridge, MA 02142

Event on Meetup: https://www.meetup.com/Boston-Area-Group-for-Informatics-and-Modeling/events/259399520/

Abstract:

Most computational methods that can be applied during drug discovery require a protein structure. Ideally, such structures are derived from experimental approaches such as X-ray, EM or NMR. However, frequently, an experimental structure of the specific protein of interest is not available. In such a case we turn to homology modeling.

The state-of-the-art for homology model prediction has progressed tremendously over the past two decades. Whereas useful HM models were initially only available in cases where a high-similarity homolog was available in the PDB, it is now often possible to predict such models even when the best homologs have only 15-25% similarity to the sequence whose structure is being predicted. The dramatic improvement in what is possible with HM is due to several factors, including: adoption of methods that can identify suitable low similarity templates on the basis of Markov Models, familial and other deep analysis of sequence space; the ability to incorporate multiple low-similarity templates to broadly span a target sequence; powerful approaches to model building that can handle missing structure due to lack of template, insertions and deletions; and the availability of massive compute power through processor clusters and parallelization. In many cases, the HM models that can be generated are so good—not only in terms of backbone trace, but also in such fine details as hydrogen bonding network, salt bridges, disulphide bonds, etc.—that they are suitable for downstream modeling methods.

We will present the history of HM approaches, culminating in a description of the state-of-the-art Rosetta HM workflow.


For more information on Cyrus Bench, click here.

About BAGIM (Boston Area Group for Informatics and Modeling)
BAGIM is an active community of Boston area scientists bringing together people from diverse fields of modeling and informatics to impact life and health sciences. BAGIM strives to create a forum for great scientific discussions covering a wide range of topics including data management, visualization, computational chemistry, drug discovery, protein structure, molecular modeling, structure-based drug design, data mining, software tools, and the sharing of goals and experiences. Our community is made up of participants from academia, government, and/or industry whose goal is to engage in the discussion of science involving a synthesis of theory and technology. Discussions sponsored by BAGIM are targeted to the needs and interests of informatics scientists, computational chemists, medicinal chemists, and statisticians. BAGIM also provides opportunities for networking within these disciplines as well as an arena for the dissemination of information of specific interest to the membership.
http://bagim.org

About Cyrus
Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering Cyrus Bench®, a SaaS platform for protein engineering to accelerate discovery of biologics and small molecules for the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus Bench® is based on the Rosetta software from Prof. David Baker’s laboratory at the University of Washington, the most powerful protein engineering software available. Cyrus customers include 10 of the top 20 Global Pharmaceutical firms and is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, and W Fund.
https://cyrusbio.com/

Cyrus Contact – Lucas Nivon

lucas@cyrusbio.com

206-258-6561

Cyrus Biotechnology Announces Release of Antibody Structure Prediction Software for Biologics Drug Development and Discovery

SEATTLE, WA March 5, 2019 — Cyrus Biotechnology, Inc., a Seattle-based biotech software company commercializing Rosetta, an advanced protein design platform, announced today the release of a novel Antibody Structure Prediction Software tool as part of its Cyrus Bench® platform.

“Antibodies make up the majority of Biologics, and now Cyrus users can model new antibodies in Bench®” said Cyrus CEO Dr. Lucas Nivon. “Antibody modeling in Rosetta was pioneered by a number of laboratories, especially that of Dr. Jeffrey Gray at Johns Hopkins University, but those methods have remained difficult to access. Our new offering makes these applications significantly more robust and easier to use, so both laboratory biochemists and antibody engineers can rely on them.”

Rosetta software is the world leader in protein modeling and design. Now, the most up-to-date protocols in Rosetta for antibody modeling are available in Bench®, facilitating work on a wider variety of common monoclonal antibody engineering problems. When combined with Cyrus’ protein modeling tools for predicting how protein mutations affect stability and affinity, these antibody prediction tools make possible complex workflows for improving efficacy or reducing potential liabilities in candidate antibody biologics.

The Rosetta antibody tools, successfully validated in the Antibody Modeling Assessment (AMA-II), have now been extended to accept a broader range of inputs without user intervention. Cyrus’ implementation uses machine learning to improve the accuracy of the antibody structure prediction workflow.

The new antibody homology modeling software is now available to subscribers to Cyrus Bench® and to new customers who subscribe to the Cyrus Bench® suite of tools.

https://www.businesswire.com/news/home/20190305005035/en/Cyrus-Biotechnology-Announces-Release-Antibody-Structure-Prediction

About Cyrus

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering Cyrus Bench®, a SaaS platform for protein engineering to accelerate discovery of biologics and small molecules for the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus Bench® is based on the Rosetta software from Prof. David Baker’s laboratory at the University of Washington, the most powerful protein engineering software available. Cyrus customers include 10 of the top 20 Global Pharmaceutical firms and is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, and W Fund.

Cyrus Contact – Lucas Nivon

lucas@cyrusbio.com

206-258-6561

Cyrus Bio announces full release of rapid and accurate protein mutational free energy tool in Cyrus Bench

Seattle, WA, January 7, 2019 – Cyrus Biotechnology, Inc., a Seattle-based firm offering access to Rosetta, the most advanced and validated software available for protein modeling and accelerated drug discovery, announced today the general release of an improved tool to predict the effect of sequence mutations on protein stability. This new software allows Cyrus customers to easily and rapidly triage thousands of potential mutations for a candidate protein molecule, in turn reducing the time and expense of experimentation. The result is more efficient discovery of stable, active, and effective Biologic drugs and other proteins.

The new mutational free energy software, herewith termed “ddG II”, replaces the existing free energy ddG tool in Cyrus Bench®. All current customers have immediate access to ddG II, and new customers can access this function simply by subscribing to the Cyrus Bench® suite of tools. 

The result of several years of work, ddG II improves on the original ddG calculation approach in Rosetta and Bench in a number of ways, including: 

  • More precise control of atomic movement
  • An improved Rosetta energy function
  • New algorithms to optimize mutations to and from proline. 

The new method has been benchmarked across a newly curated set of over 750 mutations chosen to evenly represent a broad range of different types of mutational changes. 

  • On this new benchmark set, ddG II provides a 20% improvement in rank ordering over the original ddG, as measured by the Predictive Index(1)
  • It improves categorization, as evaluated by the AUC from ROC analysis(2)
  • It reduces the number of egregious errors by more than 50%. 

As with the original ddG method, algorithmic efficiency and the significant parallelization accessible via Bench allow hundreds of ddG II calculations to be run per hour. 

Details of the original version of this approach are found in Park et al. 2016(3), and the new benchmarking and refinements will be expanded upon in a forthcoming publication focused specifically on the ddG II algorithm.

The newly curated benchmark set has been critical to the development of ddG II. In order to create this new set, Cyrus scientists examined existing datasets of protein mutational free energy changes and identified two significant issues with those datasets: 

  1. They tend to be overweighted by a handful of mutation types, particularly mutations to Alanine. 
  2. Some of the data suffers sign inconsistencies. 

The new dataset has been curated to address both of the above issues and then used to tune the algorithms now available as ddG II. One intuitive way to measure the accuracy of a free energy change is simply by categorization – experimentally measured values that are negative should be predicted by the algorithm as negative, positive as positive, neutral as neutral. By such a categorization measure, ddG II is significantly improved and is quantitatively better across a wide range of accuracy metrics.  

By improving accuracy while maintaining extremely high speed and throughput, and by retaining the simple graphical user interface for this method in Cyrus Bench®, these free energy capabilities are now more useful to a much broader set of scientists in both industry and academia. For example, it is very common to screen mutations using parallelized experimental methods that integrate approaches such as robotics or high throughput spectroscopic screening. However, – even the most efficient of these experimental methods require weeks or months to carry out. By contrast, the ddG module in Cyrus Bench® can evaluate thousands of variants in a day, thereby drastically reducing both the number of mutants that need to be tested experimentally and the time required to carry out this testing.

By combining speed and accuracy, researchers can use ddG in Bench to quickly test thousands of mutations, so they can focus their experimental efforts on a small set of variants instead — saving time and money while identifying better molecules in the process. These methods do not replace all work in the lab, but they make the experimentation process much more efficient, enabling more rapid discovery of valuable molecules. 

  1. Pearlman DA & Charifson P (2001) J Med Chem 44 3417-3423
  2. Fawcett T (2006) Pattern Recognition Letters 27 861–874
  3. Park H, Bradley P, Greisen P Jr, Liu Y, Mulligan V K, Kim D E, Baker D & DiMaio F (2016) J Chem Theory and Comput 12 6201-6212

Cyrus Biotechnology Inc.

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering Cyrus Bench®, a Software-as-a-Service (SaaS) platform for protein modeling and design capabilities to accelerate discovery of biologics and small molecules for the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries.  Cyrus Bench® is based primarily on the Rosetta software from the laboratory of Prof. David Baker at the University of Washington, the only protein engineering software experimentally proven to design new proteins completely via software. Cyrus customers include 10 of the top 20 Global Pharmaceutical firms and is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, the W Fund, and others. For more information please visit

Cyrus Biotech, CAD for molecules, announces new features to handle any pharmaceutical molecule

Computer Aided Design or CAD software has enabled the high technology world of machines and microchips and skyscrapers that we inhabit in 2018. This software was popularized by the aerospace industry in the late 1970’s and early 1980’s, and most modern machines and buildings are designed with CAD before being tested and manufactured.

Prior to CAD (and gender equality in the workplace, but we digress), design looked like this.

Design before CAD software

Now, in 2018, design can be handled much more efficiently and rapidly in software like Autocad (below). Fewer people are required to do the same amount of work, and more complex designs can be constructed, often objects so complex that they could not have been envisioned using paper and pencil. Objects designed in CAD can also be tested by CAD software — CAD testing can ensure that a bridge will withstand its designed load or that an airplane wing will safely handle excessive pressure.

Design using CAD software in 2017

Cyrus Bench is CAD for molecules.

Atoms are the building blocks of molecular structure. The ability to determine how these atoms are arranged allows us to understand the structure of larger molecules such as proteins, and to create new medicines. In the world of biochemistry, people have been able to “see” protein structures down to the atomic level since the late 1950’s using x-rays. In early work that required physical model building. Below, one of the key pioneers of this field, Nobel prize winner John Kendrew, is pictured building such a model. A very limited amount of early software aided in building these models, but they were mostly created through painstaking work and mathematical models combined with laboratory measurements. These tools did not allow for the design of new protein drugs, the way engineers and architects design new machines and buildings. Protein CAD was not yet a reality.

Building protein models (of myoglobin) before modern software, with Nobel prize winner and pioneer of x-ray crystallography John Kendrew
Copyright by the Laboratory of Molecular Biology in Cambridge, England.

Starting in the mid 1970s, methods to model proteins were developed, using the principles of physics. These could not design new protein drugs. In the 1990’s a new approach that used both physics and statistical approaches was pioneered by Professor David Baker at the University of Washington — this became known as the Rosetta software package. In the late 1990’s and early 2000’s, scientists used Rosetta to correctly predict protein structures for the first time. By 2010 scientists proved they could use Rosetta to design new useful proteins, just as architects design new buildings using CAD. By 2018 two of these Rosetta-designed molecules are being tested in human clinical trials and are on the pathway to eventually becoming drugs.

CAD for protein molecules had finally been born.

But there was a catch, Rosetta is very challenging to use, requires years of training, thousands of computers, and requires other software in order to run correctly.

At Cyrus we have taken the next step by extending Rosetta with a web based software-as-a-service (SaaS) interface running on the cloud, designed for scientific users. Cyrus Bench is pictured below — just like Autodesk AutoCAD or Dassault SolidWorks before it, Bench democratizes CAD for protein molecules to all protein engineers and scientists.

Cyrus Bench CAD software in a web browser

Cyrus Bench CAD is now for all molecules.

This week Cyrus Biotech is announcing a major step forward for our main product Cyrus Bench: Support for small molecule ligands. We have announced this in a separate Press Release Here.

In this section we explain this new addition to our software in simple, non-scientific language.

Drugs have been used by humans for millennia, and modern drugs from the Pharmaceutical and Biotech industries are more powerful than ever — they prevent viral attack, halt deadly bacterial infections, keep asthmatics breathing, keep diabetics alive, tame the ravages of mental illness, put cancer in remission, and help us to live long and healthy lives.

At an atomic level, drugs are either small molecules or Biologics–names that reflect their relative sizes. Small molecule drugs are typically comprised of fewer than a few dozen atoms. Proteins, in contrast, can be as large as 20,000 or more atoms.

Protein-based drugs make up most so-called Biologic drugs — these are vaccines against deadly infections, monoclonal antibodies that extend the lives of cancer patients and therapeutic proteins like insulin for diabetics. A typical antibody molecule is pictured below. Other than biologics, all other drugs are small molecules, making up 75% of all drug sales. As an example, below we show Aspirin, an ancient medication (about 2400 years in human use) that is also perhaps the most famous small molecule drug.

Cyrus Bench is based on Rosetta, which in its standard state only handles proteins efficiently, but does not have automated tools to accommodate small molecules.. Up until this week, Rosetta could only conveniently handle proteins, and could therefore be used for modeling less than 5% of all drugs.

This week all of that is changing.

An antibody protein or Biologic drug

A well-known small molecule drug, Aspirin

 

 

 

 

 

 

 

 

 

 

 

We are announcing Cyrus’s partnership with Openeye Scientific Software, a pioneer and leader in the modeling of small molecules with a special focus on high-impact applications in the Pharmaceutical industry. Over the last 24 months Cyrus scientists and software developers have worked to integrate and automate small molecule handling from Openeye into Cyrus Bench.

A drug target with a candidate small molecule loaded in Bench

As of this week, for the first time, biochemists without years of highly specialized computational experience can model small molecules inside proteins using Rosetta in Cyrus Bench. This makes the large majority of drugs — small molecules — accessible to users across Pharma, Chemicals, Consumer Products, and Academia. We are rolling this capability out to a select group of early customers before launching general availability later this year.

We are very excited to see what new drugs can be discovered, diseases cured, and lives improved or even saved using Cyrus Bench!

Dr. Lucas Nivon, CEO, Cyrus Biotechnology

Cyrus Biotechnology and OpenEye Scientific Software Announce Collaboration and Cheminformatics Integration to Expedite New Drug Design and Development with Cyrus Bench Platform

SEATTLE, WA October 30, 2018 — Cyrus Biotechnology, Inc., a Seattle-based biotech software company commercializing Rosetta, an advanced protein design platform, announced today that through a collaboration with OpenEye Scientific Software, Inc., a leader in computational molecular design, capabilities have been developed that allow small molecule ligands to be processed and used with Rosetta and within the Cyrus Bench® platform for computational protein drug design.  

“We are very excited to integrate these new ligand tools in our protein design platform,” said Cyrus CEO Dr. Lucas Nivon. “Previously scientists have had to endure incompatible tools and sub-par results when carrying out protein-ligand modeling, but with the new automated small molecule integration, we have created a straightforward and reliable tool our customers can use to design new therapeutics and industrially useful enzymes.”

Rosetta software is the world leader in protein modeling and design. However, including small molecule ligands when using Rosetta has been problematic, severely limiting its utility for many pharmaceutical, consumer products and other applications where protein/small-molecule interactions are critical.

Cyrus has developed new scientific tools that integrate OpenEye’s cheminformatics and modeling technologies to allow Cyrus customers to:

  • Parameterize small molecules robustly and with high accuracy
  • Carry out enzyme and general protein design in the presence of a ligand.  

OpenEye CEO, Dr. Anthony Nicholls, said, “We are excited to be a part of Cyrus Bench® by providing OMEGA, the world’s best validated and industry-leading conformer generation tool, along with OpenEye’s robust and highly performant cheminformatics and modeling

capabilities. We look forward to seeing the science both companies will enable by this partnership.”

OpenEye has been a leader in cheminformatics and molecular modeling for over twenty years. OpenEye’s toolkit platform allows flexible and powerful workflow integration with Cyrus Bench and Rosetta software. Robust and seamless support for state-of-the-art small molecule/protein interactions is now available to Bench users.

This software integration has been tested and debugged on thousands of examples from the Protein Data Bank and will robustly allow small molecules to be included in most Rosetta calculations in Bench.

This new set of tools for protein modeling in the presence of arbitrary small molecules—utilizing a simple-to-use Rosetta GUI–is now available to existing subscribers to Cyrus Bench® and can be accessed by new customers by subscribing to the Cyrus Bench® suite of tools.

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering protein modeling and design capabilities to the Biotechnology, Pharmaceutical, Chemical, Consumer Products and Synthetic Biology industries. Cyrus was founded in 2014 as a spin-out from the University of Washington, and offers Cyrus Bench®, a Software-as-a-Service (SaaS) platform for protein structure prediction via homology modeling, protein modeling, protein stabilization, protein engineering and protein design to accelerate discovery of biologics and small molecules. Cyrus Bench is based primarily on the Rosetta molecular modeling and molecular design software package from the laboratory of Prof. David Baker at the University of Washington, along with associated software. Cyrus Bench offers the world-leading protein structure prediction pipeline of Rosetta and SparksX, the top structure prediction software in the bi-annual CASP competition and the weekly CAMEO competition, as well as the only protein engineering software experimentally proven to design new proteins completely via software. Cyrus customers include 10 of the top 20 Global Pharmaceutical firms as well as smaller Biotechnology and Chemicals firms. Cyrus is financed by leading investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Venture Investments, the W Fund, and others. For more information please visit

https://cyrusbio.com/  

OpenEye Scientific

OpenEye is a scientific leader in computational molecular design based on decades of delivering useful applications and programming toolkits. Our scientific approach changed perception of what’s possible with the speed, robustness and scalability of our tools. OpenEye recently released Orion, the only cloud-native fully integrated drug discovery platform, combining unlimited computation and storage with powerful tools for data sharing, visualization and analysis in an open development platform.  Founded in 1997, OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, NM, with offices in Boston, Cologne and Tokyo. For more information please visit https://www.eyesopen.com

NOTICE: The information contained in this document is dated as of October 30, 2018.  Cyrus Biotechnology, Inc. (the Company) disclaims any obligation to update such information after such date.  This document contains forward–looking statements reflecting the Company’s current expectations that necessarily involve risks and uncertainties.  Actual results and the timing of events may differ materially from those contained in such forward-looking statements due to a number of factors and the Company undertakes no obligation to revise or update any forward-looking statement to reflect events or circumstances after the issuance of this press release.

Cyrus Press Release 10/30/2018

Cyrus Contact – Lucas Nivon
lucas@cyrusbio.com
206-258-6561

OpenEye Contact – Fred Livingston
info@eyesopen.com