Complete Suite

Bench delivers a full array of molecular modeling  software, e.g. sequence and structure alignment, to use Rosetta to its full potential.

Cloud Deployment

Thousands of CPUs, instant updates, massive databases, all at the touch of a button. Your data is private and encrypted, and all data for sequences and biological structures belong to the user, unlike with public servers.

Custom GUI

Cyrus’ Rosetta interface (GUI) was designed from scratch to be powerful but intuitive to a biochemist or chemist, making complex tasks accessible via a web browser.

Automated Pipelines

State-of-the-art protein modeling usually requires multiple complex steps with millions of files. Cyrus automates and simplifies these workflows so you can focus on the science.

Cyrus Bench includes the features most
requested by BioPharma scientists


Cyrus Overview

An introduction to Rosetta protein modeling and engineering software, and Cyrus’ software and services

Cyrus in drug discovery

A summary of practical applications of Rosetta and Bench focused on clinical applications

Cyrus Scientific Validation

An overview of scientific studies validating Rosetta software in vitro and in vivo

Cyrus Software Demo

An in-depth sample use case demo of Bench showing how to run a protein stabilization calculation on a therapeutic candidate enzyme

Bench is available now. It offers the most in-demand features from Rosetta, including:

  • Basic protein design tools in Rosetta, the same tools responsible for an array of “firsts” in protein design, including the first fully-computational protein design (top7) and first computational design of a protein-protein interaction with stronger binding than an antibody (HB36).
  • Protein mutational free energy (ddG) calculations using Rosetta’s unique backbone flexibility modeling.
  • Protein/protein interface redesign with fixed or flexible backbone, methods used for Biologics optimization in academia and Big Pharma, as presented in multiple conferences and published papers.
  • Protein loop structure prediction / protein loop modeling using the latest NGK protocol in Rosetta
  • Protein/small molecule ligand interface design, for engineering of natural enzymes or small molecule binding proteins for therapeutic or other biotech tools use cases.
  • Modeling of protein/small molecule structural fluctuations, similar to molecular dynamics (MD) for analysis of small molecule drug complexes, in partnership with Openeye Scientific. Very useful for detailed analysis of protein/ligand docking or virtual screening output in a Computer Assisted Drug Design (CADD) workflow.
  • Protein immunogenicity prediction (Biologics immunogenicity). Machine learning based MHC-II (T-cell) epitope prediction for triage and optimization of Biologics candidates. Contact us for information about our highly automated structure-based deimmunization or epitope removal for Biologics candidates.
  • Antibody Structure Prediction / Antibody Homology Modeling. Cyrus’ version of the extensively validated RosettaAntibody tool out of Jeff Gray’s lab at Johns Hopkins, with a Machine Learning workflow to automated nearly any input antibody Fv sequence.
  • More features coming soon including Homology Modeling with user templates, Homology modeling with a small molecule ligand, protein/protein docking (general and antibody/antigen docking) and more.


If you are with a non-profit, academic or government organization you can learn more about our academic plans here.

Start a free one month trial of Cyrus Bench now, no payment info required.