Cyrus Biotechnology Exhibits at the PEGS Protein Engineering Summit in Boston, May 1st-4th

SEATTLE, April 20, 2017 — Cyrus Biotechnology, Inc., a new 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 13th Annual PEGS Boston Protein Engineering Summit in Boston, from May 1st through May 4th.

Dr. Yifan Song, Chief Science Officer 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 503 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 (single point mutants, multiple point mutants, evolutionary redesign)
  • Protein / Protein Interface Design
  • Protein Design (modifications to function or structure)
  • Enzyme Optimization

 

Background

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a new 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.

 

NOTICE: The information contained in this document is dated as of April 19, 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 04/20/2017

 

Cyrus Biotechnology Presents Implementation of Biocomputing on the Cloud at the American Chemical Society Spring Meeting in San Francisco

SEATTLE, April 3, 2017 — Cyrus Biotechnology, Inc., a new 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 to the American Chemical Society Spring Meeting in San Francisco on April 3rd, 2017.

Dr. Lucas Nivon, CEO of Cyrus Bio, will speak about Cyrus’s journey of deploying the Rosetta software on the cloud and share lessons learned. The Rosetta software, from the RosettaCommons, is the premier software platform for advanced computational protein engineering. It is a very complex software stack that requires years to learn in depth, is difficult to document, and is constantly in flux as new scientific features are created.

Cyrus has implemented the Rosetta stack on a public computing cloud, resulting in higher quality software with far higher performance in a secure multi-tenant model. R&D organizations can remove large capital expenditures, avoid over- or under-provisioning, and maximize scientific output.

Scripting or computing queues are no longer needed for structural biologists and biochemists who want to do protein design or modeling without having advanced computational skills.

Scientific computing is diverse, requires high performance and does not trivially extend to the cloud. It requires cloud-based systems architected specifically for scientific computing, using modern web technologies and frameworks, such as high performance web frontends and backend job provisioning.

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 continue 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 (single point mutants, multiple point mutants, evolutionary redesign)
  • Protein / Protein Interface Design
  • Protein Design (modifications to function or structure)
  • Enzyme Optimization

Cyrus Bio wishes to thank Dr. Veerabahu Shanmugasundaram, one of the session’s organizers, for his kind invitation to speak at the Meeting.

 

Background

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a new 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.

 

NOTICE: The information contained in this document is dated as of January 10, 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 04/03/2017

Cyrus Biotechnology supports the Boston Area Group for Informatics and Modeling

SEATTLE and BOSTON, January 10, 2017 — Cyrus Biotechnology, Inc., a new 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 support the Boston Area Group for Informatics and Modeling (BAGIM).

With over 700 members and 17 industrial sponsors, BAGIM is one of the most preeminent and active professional communities in the Boston area, focusing on computer based modeling, facilitating information exchange and networking through presentations of scientific relevance by luminaries from industry and academia. In 2016, BAGIM has hosted nine well attended scientific presentations and networking events and continues to maintain an active presence on social media such as LinkedIn, Meetup, and Facebook.

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 continue 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 (single point mutants, multiple point mutants, evolutionary redesign)
  •  Protein / Protein Interface Design
  •  Protein Design (modifications to function or structure)
  •  Enzyme Optimization

Cyrus is pleased to support BAGIM ‘s efforts to advance biological informatics and modeling. Sponsorship from Cyrus will contribute to BAGIM expenses related to its educational/networking initiative centered around a lecture series.

Background

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.

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a new 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 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.

 

NOTICE: The information contained in this document is dated as of January 10, 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 2017.01.10

Cyrus Biotechnology CEO to Unveil Cyrus Bench software for Protein Modeling and Design

SEATTLE, WA, December 20, 2016 — Cyrus Biotechnology, Inc., a new biotechnology software company offering the most advanced protein modeling and design capabilities to the Biopharmaceutical, Synthetic Biology, Chemical, and Consumer Products industries is presenting at the Biotech Showcase January 9 at 5:15PM in San Francisco.

Dr. Lucas Nivon, CEO of Cyrus, will present an overview of the Cyrus Bench software package, which is already used by customers in the BioPharma and Chemical industries including many Fortune 500 firms. The presentation will show use cases based on real customer examples, and highlight the impact that Cyrus Bench can make in accelerating product discovery.

Cyrus Bench automates the Rosetta software suite developed by the RosettaCommons consortium. Bench makes the most advanced biotechnology software available to most industry users for the very first time. 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 (single point mutants, multiple point mutants, evolutionary redesign)
  • Protein / Protein Interface Design
  • Protein Design (modifications to function or structure)
  • Enzyme Optimization

Background

Cyrus Biotechnology

Cyrus Biotechnology, Inc. is a new 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 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.

NOTICE: The information contained in this document is dated as of 12/20/2016.  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 2016.12.20

Cyrus CSO Yifan Song publishes advance in CryoEM Structure

Cyrus CSO Yifan Song, along with lead author Ray Wang from the University of Washington and PI Frank DiMaio have published an important next step in the progress towards making Cryo-Electron Microscopy (cryo-EM) a vital new tool in drug discovery. In their manuscript published in the journal eLife, “Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta”, Wang and co-authors describe a method in Rosetta software to automatically build atomic resolution models of complex protein assemblies from cryo-EM data. Cryo-EM technology has improved drastically in recent years due to new detector technology, allowing this method to approach atomic resolution. Atomic resolution is vital in solving protein structures, and structures are a linchpin in the discovery of most modern drugs. Without Rosetta, cryo-EM models from the new detectors are valuable, but with Rosetta automated structure building of atomic-resolution models, these data are drastically more useful in solving important medical problems.

https://elifesciences.org/content/5/e17219

Cyrus CTO Javier Castellanos featured in Chile Global

Cyrus’s CTO Javier Castellanos was featured in a story on Chile Global, the website of a Chilean entrepeneur’s group focused on connecting Chileans who are making a big impact abroad with their home country. The article describes Javier’s path from being a Biochemistry undergrad in Chile to co-founding Cyrus Biotechnology. It focuses on the key role his work in Prof. David Baker’s lab played in growing Javier’s interest in protein design, and how Cyrus was conceptualized as a mission to bring more powerful tools to users outside of academia. The full article is below, and is in Spanish, but Google Translate does a decent job of translating it automatically.

http://www.chileglobal.net/doctor-javier-castellanos-estamos-tratando-de-abrir-un-mercado-de-medicamentos-que-hoy-en-dia-no-existe/

Designing cyclic peptides! Congrats UW IPD, Cyrus Co-Founders Yifan Song & David Baker

Scientists in the UW IPD and David Baker’s lab there have been designing mini-proteins up to 120 residues over the last few years, in a slew of exciting research papers in protein design. Now for the first time they’ve designed short cyclic peptides in the range 18-47 residues — constrained for example by N to C terminal cyclization. Cyclic peptides in nature have evolved into a wide variety of binding modalities, and they are therefore of great interest as drug candidates. Twelve cyclic peptides are designed and have their structures confirmed by experimental methods in this tour de force manuscript. Cyrus co-founder Yifan Song is a co-author on this combined computational and wet lab work.

Read the original article at Nature’s website:

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature19791.html

Cyrus, UW IPD and Baker lab in Geekwire

Xconomy hosted Cyrus, Prof. David Baker of the University of Washington’s IPD, and founders of two other spin-outs from the IPD, Virvio and PVP Biologics, at their EXOME mini-symposium in Seattle. Geekwire gives a great summary of the current state of computational protein design.

 

Happy April 1! Announcing Cyrus ROSVAC-2!

Seattle, WA, April 1 2016. Cyrus Biotechnology is proud to announce a major step forward in computer biochemistry, the ROSVAC-2, an industrial-strength minicomputer custom-designed for simulations of biological molecules, with an astonishingly small 2000 sq ft. footprint, capable of over 5 simultaneous protein amino acid sequence calculations per annum.
UNIVAC-I1951
Data is input into ROSVAC-2 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-2 displays protein cartoon structures in beautiful 128×128 black and white pixels (ROSVAC-2 operator control booth pictured below). ROSVAC-2 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-2 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-2 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-2 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-2, but is in beta testing for our  best-in-class cloud-based protein modeling and design tool, Cyrus Bench based on Rosetta, with general release in mid 2016. Contact us at info@cyrusbio.com if you would like to learn more.

Cyrus Biotechnology licenses advanced biochemistry software from Indiana University to deliver world-leading protein structure prediction engine

Cyrus offers an easy-to-use cloud pipeline using SparksX software package to accelerate drug development

Seattle, and Indianapolis, October 8, 2015 – Cyrus Biotechnology has signed a software licensing agreement with Indiana University Research and Technology Corporation (IURTC) at Indiana University (IU) to commercialize the SparksX software package developed at the lab of former IU professor Yaoqi Zhou at the Indianapolis campus.

Cyrus offers a highly automated protein structure prediction and design software-as-a-service (SaaS) package, “Cyrus Bench”, for both bench scientists and computational biologists/chemists.

SparksX, combined with Rosetta from David Baker’s lab at the University of Washington (UW) and licensed to Cyrus, leads the competition in protein homology modeling, both in the biennial CASP and weekly CAMEO “blinded” competitions.

SparksX, developed by Zhou and his team, recognizes protein folds and identifies “deep” (difficult to detect) protein sequence similarity, or homology, better than any other software package, winning first place in CASP 6.

The Cyrus founding team brings decades of protein modeling and high-performance computing experience, with UW Professor David Baker, scientific advisor, Lucas Nivon, CEO, Yifan Song, CSO, Javier Castellanos, CTO.

“As a powerful tool for molecular modeling, SparksX is positioned to help further establish Cyrus as a leader in the drug development space. They have a suite of products that were originally developed through academic work across multiple universities, and Cyrus is a fine example of how startup ventures can further the impact of such research and translate these developments into the marketplace. We are delighted to partner with the Cyrus team to bring the SparksX software to market”, said Marie Kerbeshian, VP of Technology Commercialization at IURTC.

Full Release