9. Support & Resources
9.1 FAQ
Ariax Bio Questions
Q: Why should I use Ariax Bio?
At Ariax Bio, our mission is to enable anyone the ability to access the best protein design tools in the world without barriers, including cost, access to specialized hardware, or technical expertise. With our platform, users can easily setup protein design projects with unparalleled speed but at the lowest prices in the industry. For most users who lack access to GPU hardware, protein design jobs on Ariax Bio may be less expensive than manually running jobs on cloud GPU providers. There are no strings attached, no sales calls or onboarding, and no subscriptions. Visit our Why Ariax page for more details.
Q: Who owns the intellectual property for proteins designed using Ariax Bio?
All intellectual property rights to proteins designed using Ariax Bio belong exclusively to the user. Ariax Bio explicitly disclaims any ownership or rights to user-designed sequences or structures. Managing intellectual property protection, including patentability, is solely your responsibility.
Q: How does Ariax Bio handle data privacy and confidentiality?
User privacy is a top priority at Ariax Bio. We never share your data with third parties, and we intentionally avoid collecting or storing sensitive project details like target IDs or sequences. All input files and design results are stored in a secure, private cloud location under your control. Files are anonymized with generic names, and you can delete your data at any time. Ariax Bio staff may access these files only to provide technical support.
Q: How do I purchase compute credits?
A: You can purchase compute credits directly from our platform after logging in. We offer two convenient ways to pay: by credit card for immediate access (credits available instantly), or by requesting a quote for a purchase order (credits typically available within 24 hours of PO receipt by our finance team). Both options are available on the Billing page.
BindCraft Questions
Q: What is BindCraft?
BindCraft is an open-source pipeline for automated protein binder design, developed by Dr. Martin Pacesa in the lab of Prof. Bruno Correia. It integrates AlphaFold2 backpropagation, ProteinMPNN, and PyRosetta to generate high-quality binders against user-defined protein targets. With minimal setup, users can run hundreds to thousands of design trajectories, apply stringent structural and interface filters, and output a ranked list of experimentally tractable candidates. For more details, see the BindCraft preprint on bioRxiv.
Q: Why does Ariax Bio use BindCraft instead of other protein design tools?
A: BindCraft stands out as a leading platform for de novo protein design, both in published benchmarks and in our own hands-on experience. In multiple rounds of Adaptyv’s protein design competitions (see results here, and here), BindCraft-derived designs have consistently outperformed alternatives. In the most recent Adaptyv competition, 6 out of the 7 de novo miniprotein binders that successfully bound their target were generated using BindCraft. We also have extensive real-world experience with BindCraft in our own research, achieving a high success rate for bona fide binders—giving us direct confidence in its capabilities.
Another key feature of BindCraft is that it automates the entire design process, eliminating the need for manual intervention. This full automation makes it robust and accessible for any researcher, not just specialized protein designers.
Finally, BindCraft is open-source, comes with excellent documentation, and has seen rapid and widespread adoption in the protein design community. For all these reasons, BindCraft is the first and best example of the kind of protein design platform we aim to offer at Ariax: robust, open-source, and easy to use for any scientist.
Q: How long does a BindCraft design run typically take and how much will it cost?
Several factors influence the duration of a BindCraft design run, including the size of the target, complexity of the desired hotspot, and the number of accepted designs requested. Filters applied also affect runtime; relaxed filters allow more designs and faster completion but may increase experimental failure risk. Project speed depends on GPU type, with more powerful GPUs generally resulting in faster runs. Typical completion times range from 24-72 hours for 100 designs.
As project costs are entirely based on GPU usage, the same factors that affect runtime will also impact cost. In general, typical jobs (100 accepted designs) will range from ~$100 for small proteins targets (<100 amino acids) to $300-500 for larger targets (<300 amino acids). Try to trim your protein structure template to the minimum necessary amino acids. We also recommend monitoring progress initially to optimize runtime and costs based on hotspot selection and filter settings.
Q: What is the difference between a "trajectory" and an "accepted design"?
A trajectory is a single design attempt generating a binder structure and sequence using AlphaFold2, preparing it for refinement with MPNN. Trajectories are exploratory and may not yield usable designs. An accepted design is an optimized trajectory that passes all quality filters—such as confidence scores, interface metrics, and structural properties—and is saved for potential experimental validation. Typically, users execute hundreds or thousands of trajectories to produce dozens of accepted designs, which are ranked and stored separately.
Q: What licenses are required to use BindCraft?
BindCraft uses PyRosetta, which is free for academic and non-profit institutions and is available to commercial users for a fee. Academic and non-profit users can view the non-commercial license agreement. Commercial organizations can find more information about obtaining a PyRosetta commercial license.
9.2 Contact:
- Info: info@ariax.bio for general questions, comments, or information about Ariax Bio.
- Support: support@ariax.bio for assistance with projects, platform usage, and troubleshooting.
- Billing: finance@ariax.bio for questions related to billing, purchase orders, and payments.
- Community: Join our Discord server at discord.gg/Q7SnVE3ujQ for peer support and discussion.