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://www.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

Cyrus Biotechnology to Present at the Immunogenicity & Bioassay Summit on October 25, 2018

SEATTLE, WA October 12, 2018 — Cyrus Biotechnology, a Seattle-based firm offering access to Rosetta, the most advanced software available for protein modeling and accelerated drug discovery, announced today that it will present at the 10th Annual Immunogenicity & Bioassay Summit, to be held in Washington DC on October 22-25, 2018.

Dr. Indigo King, a computational protein design and immunology specialist, will present at the Immunogenicity Summit as follows:

Abstract: Computational protein design has the potential to create a novel class of therapeutics with tunable biophysical properties, but immunogenicity remains a concern. We have combined machine learning with structure-based protein design to identify and redesign T-cell epitopes without disrupting function of the target protein or creating new epitopes. We have verified the method experimentally, removing T-cell epitopes from a gene therapy target, an immunotoxin, and GFP while maintaining folding and function.

Date: Thursday, October 25th, 2018

Time: 3:25 PM EDT

Track: Immunogenicity Prediction & Control

Room: Edison ABC

Venue: The Westin Alexandria, 400 Courthouse Square, Alexandria, VA 22314

For more information on immunology with Cyrus, see Cyrus Biotechnology Launches Immune Epitope Prediction Software.

 

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering protein modeling and design capabilities to the Biopharmaceutical, 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, modeling, stabilization, engineering and design to accelerate discovery of Biologics and Small Molecules. Cyrus Bench is based primarily on the Rosetta software package from Prof. David Baker’s lab at the University of Washington, along with associated software. Cyrus Bench offers the world-leading protein structure prediction pipeline of Rosetta, as well as the only protein engineering software experimentally proven capable of designing entirely new proteins. Cyrus Bench is powered by Rosetta, which has been developed over near 20 years, and validated by well over 700 publications that demonstrate efficacy both in vitro and in vivo. Cyrus is financed by experienced investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Real Estate, the W Fund, and others.

NOTICE: The information contained in this document is dated as of October 12, 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 10/12/2018

 

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

Cyrus Biotechnology Appoints Jake Litwicki as VP of Engineering

Cyrus growing its team to speed biologics and small molecule
drug development software to market

SEATTLE, WA August 6, 2018 — Cyrus Biotechnology, a biotechnology software company
offering first-in-class tools for advanced protein modeling and discovery in drug development,
announced today the appointment of Jake Litwicki as VP of Engineering. Jake will lead software
engineering for the Cyrus Bench Software as a Service platform which speeds development of
new drugs and products sold to client firms in pharmaceuticals, biotechnology therapeutics,
synthetic biology and consumer products. Jake’s team will continue to grow the Cyrus Bench
toolkit, and add valuable new features including tools for antibody and biologics discovery as
well as small molecule modeling and discovery.  Prior to joining Cyrus Jake led software
engineering teams and spearheaded the transition to more modern cloud architectures at a
custom software development firm, a marketing technology startup, and most recently as the
leader of the Platform, Global and Microservice teams at Sterling Talent Solutions.
“Jake is a seasoned technical leader with experience across a variety of company and team
sizes, with a proven ability to bring widely used software to the market and to drive
improvement and best practices in an engineering organization,” said Dr. Lucas Nivon, CEO of
Cyrus. “Jake’s passion for software engineering, architecture and leadership will make him an
important part of our growth as we add scientific users at companies worldwide.”
“Cyrus is a unique organization with the potential to literally change the world for the better.
Having the opportunity to contribute to something with that kind of impact is truly inspiring”,
said Jake.  “I am eager to help grow and evolve the Cyrus team into a world leader in both
biotechnology and software as a service”, he added.

Jake’s team at Cyrus will be responsible for software frontend, backend, testing and release of
new scientific features developed by the open source RosettaCommons community, by other
Cyrus partners, or by Cyrus’s scientific software development and infrastructure team. Cyrus
software and services are currently being utilized by multiple companies including 10 of the top
20 Global Pharmaceutical firms, not only to design new drugs but also to offer solutions for
problems in drugs already under development.

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, modeling, stabilization, engineering and design to accelerate
discovery of Biologics and Small Molecules. Cyrus Bench is based primarily on the Rosetta
software package from Prof. David Baker’s lab 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 in
financed by leading investors in both Technology and Biotechnology, including Trinity Ventures,
Orbimed, Springrock Ventures, Alexandria Venture Investments, the W Fund, and others.

Cyrus is featured in: Built In Seattle’s 50 Startups to Watch in 2018

Cyrus Biotechnology offers molecular scientists a cloud-based platform that allows them to design and build protein molecules. The software is based on a protein-modelling platform called Rosetta, which was first conceived and created at the University of Washington, and essentially allows the creation of entirely new types of proteins inside a computer. Cyrus Biotechnology brings this capability to the market with a software package which includes, among other things, a visual representation of proteins as a user constructs them.

Click here for full article.

Cyrus Biotechnology Launches Immune Epitope Prediction Software

SEATTLE — Cyrus Biotechnology, Inc., a Seattle-based firm offering access to Rosetta, the most advanced software available for protein modeling and accelerated drug discovery, announced today the general release of a new immune screening and prediction tool in their Cyrus Bench® platform.

Cyrus customers can now drastically reduce immunogenicity in pre-clinical candidates, thereby decreasing the chance of dangerous and costly adverse events during clinical trials.

Published work has demonstrated the effectiveness of combining this epitope prediction method with the powerful protein design algorithms in Rosetta. Two published examples show positive proof of drastic immunogenicity reduction, both in mice and ex vivo in human test subjects. Cyrus has carried out a third such study with an academic collaborator, which has been experimentally proven in animal models. The details of this study will be published separately.

The epitope prediction software is based on the carefully curated set of known MHC-II epitopes in the IEDB database. Those data were used to train a modern Machine Learning algorithm to detect likely new epitopes in proteins of interest. The algorithm was then refined with experimental data to confirm its scientific validity.

The immune epitope prediction and protein design algorithms are currently available to existing subscribers to Cyrus Bench® and can be accessed by new customers by subscribing to the Cyrus Bench® suite of tools.

Cyrus will introduce a novel, fully automated immune epitope removal software tool in the next few months as another valuable addition to the rapidly expanding capabilities in Cyrus Bench®. It will be the first commercially available software-based method proven to reduce immune liabilities in candidate biologics or already marketed biologics.

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering protein modeling and design capabilities to the Biopharmaceutical, 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, modeling, stabilization, engineering and design to accelerate discovery of Biologics and Small Molecules. Cyrus Bench is based primarily on the Rosetta software package from Prof. David Baker’s lab 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 Bench is based on over 15 years of biochemistry software development and over 700 published papers demonstrating experimental efficacy in vitro and in vivo. Cyrus in financed by experienced investors in both Technology and Biotechnology, including Trinity Ventures, Orbimed, Springrock Ventures, Alexandria Real Estate, the W Fund, and others.

NOTICE: The information contained in this document is dated as of July 10, 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.

Business Wire Release July 10, 2018

Contacts

Cyrus Biotechnology, Inc.
Lucas Nivon, 206-258-6561
lucas@cyrusbio.com

Cyrus Biotechnology Exhibits at the PEGS Protein Engineering Summit in Boston, April 30th – May 3rd

SEATTLE, April 18, 2018 — Cyrus Biotechnology, Inc., a biotechnology software company offering the most advanced protein modeling and design capabilities to the Biopharmaceutical, Synthetic Biology, Chemical, and Consumer Products industries is pleased to announce its participation in the 14th Annual PEGS Boston Protein Engineering Summit in Boston, from April 30th through May 3rd.

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. 

The Rosetta software package, from the RosettaCommons, is the premier software platform for advanced computational protein engineering. Cyrus has implemented the Rosetta stack with an easy to use interface on a public computing cloud, resulting in high reliability software with high performance and usability in a secure multi-tenant model. R&D organizations can remove large capital expenditures, avoid over- or under-provisioning, and maximize scientific output.

In silico modeling and design of proteins is becoming increasingly relevant to the pharmaceutical industry, as investment in research, development and clinical trials of biologic therapeutics continues to grow. Cyrus Bench® software, and the underlying Rosetta software package, are already leveraged by many global pharmaceutical organizations and are at the nexus of this major trend. 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)
  • Protein Stabilization
  • Computational Affinity Maturation (Interface Design)
  • Prediction of Immunogenic Epitopes
  • Removal of Identified Liabilities
  • Protein Structure Optimization and Design
  • Antibody Engineering
  • Antigen Design

 

Background

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering protein modeling and design capabilities to the Biopharmaceutical, 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, modeling, stabilization, engineering and design to accelerate discovery of Biologics and Small Molecules. Cyrus Bench is based primarily on the Rosetta software package from Prof. David Baker’s lab 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 Bench is based on over 15 years of biochemistry software development and over 400 published papers demonstrating experimental efficacy in vitro and in vivo. Cyrus is funded by experienced investors in Tech and Biotech including Trinity Ventures, Orbimed Advisors, SpringRock Ventures, W Fund and others.

NOTICE: The information contained in this document is dated as of April 18, 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 04/18/2018

 

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

Cyrus Bio Co-Founder David Baker Featured in the New York Times

SEATTLE, WA January 02, 2018 — Prof. David Baker, Cyrus Bio Scientific Co-Founder and Director of the Institute for Protein Design at the University of Washington, and the Rosetta software, have been prominently featured in the December 26th, 2017 New York Times article by Carl Zimmer, “Scientists are Designing Artisanal Proteins for Your Body.”

The article illustrates how computationally building proteins from first principles are effectively targeting influenza, botulism, opioids, gluten intolerance, gene therapy and immuno-oncology.

Gary Nabel, Chief Scientific Officer at Sanofi, is quoted saying that “the new research may lead to the invention of molecules we can’t yet imagine.”

Cyrus Bench® is a Software-as-a-Service platform based on the Rosetta protein modeling toolkit for protein structure prediction, discovery, modeling, stabilization, engineering and design, making some of the methods developed at Prof. Baker’s lab available to a wider audience of scientific users in Pharmaceutics, Chemicals, Consumer Products, Academia and Non-Profits.

Click here to access the article. A subscription to the New York Times may be required.

 

Cyrus Biotechnology to Present at the Biotech Showcase™ Annual Conference on January 9, 2018

Cyrus Bio technology can speed new drug discovery

 

SEATTLE, WA December 29, 2017 — Cyrus Biotechnology, a biotechnology software company offering first-in-class tools for advanced protein modeling and discovery in drug development, announced today that it will present at Biotech Showcase™ 2018, to be held January 8–10 during the most important week in healthcare at the Hilton San Francisco Union Square.

 

Dr. Lucas Nivon, CEO, will present at the Biotech Showcase™ as follows:

Date: Tuesday, January 9th, 2018

Time: 2:00PM PST

Room: Franciscan D (Ballroom Level)

Venue:  Hilton San Francisco Union Square Hotel, 333 O’Farrell Street, San Francisco, CA

 

Cyrus offers Bench®, a Software-as-a-Service platform for protein structure prediction, biologics discovery, alternative structure modeling, protein stabilization, engineering and design, along with custom software development and experienced scientific support services in computational protein engineering.

 

Bench® is based on two decades of work in computational biophysics and the first software algorithms to design new proteins in a computer. It has been designed for a wider range of users than previous academic-based software. Cyrus is rapidly acquiring customers ranging from Fortune 500 Pharma (including eight of the top 20 Pharma firms), chemical and consumer products firms to privately-held biotech and synthetic biology firms.

 

Bench® is a graphical, cloud-enabled version of the Rosetta protein modeling toolkit. Data generated from Rosetta technology can be used in the design of new potential therapeutics, such as a therapeutic protein of Tocagen’s Toca 511 and PVP Biologics’ KumaMax, an oral enzyme. Cyrus is funded by leading investors in both Tech and Biotech sectors, led by Trinity Ventures with Orbimed, SpringRock, W Fund and others.

 

“We are very excited to be presenting at Biotech Showcase™,” said Cyrus CEO Dr. Lucas Nivon. “Year after year, our participation in the J.P. Morgan Annual Healthcare Conference has been fruitful and productive for the organizations we have established partnerships with. Our Bench® technology broadens access to the most advanced biocomputational methods, giving more scientists the means to speed their research and save costs. The result is more effective drugs getting to patients sooner.”

 

Biotech Showcase™, produced by Demy-Colton and EBD Group, is an investor and networking conference devoted to providing private and public biotechnology and life sciences companies with an opportunity to present to, and meet with, investors and pharmaceutical executives in one place during the course of one of the industry’s largest annual healthcare investor conferences, J.P. Morgan Annual Healthcare Conference.

 

Sara Demy-Colton, CEO of Demy-Colton, said: “We are delighted that Cyrus Biotechnology will be presenting at Biotech Showcase this year. Biotech Showcase is the perfect platform for life science companies to showcase their innovation and seek out their next deal. This year again we are thrilled to be hosting what we believe will be the great business development opportunity of 2018.”

 

Background

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a privately-held biotechnology software company offering protein modeling and design capabilities to the Biopharmaceutical, 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, modeling, stabilization, engineering and design to accelerate discovery of Biologics and Small Molecules. Cyrus Bench is based primarily on the Rosetta software package from Prof. David Baker’s lab 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 Bench is based on over 15 years of biochemistry software development and over 400 published papers demonstrating experimental efficacy in vitro and in vivo. Cyrus is funded by experienced investors in Tech and Biotech including Trinity Ventures, Orbimed Advisors, SpringRock Ventures, W Fund and others…

 

NOTICE: The information contained in this document is dated as of December 29, 2017.  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 12/29/2017

 

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