BindCraft2 Project Setup
BindCraft2 designs protein and peptide binders using AlphaFold2-guided optimization, ProteinMPNN sequence redesign, and structural validation. Ariax brings these steps together in a managed campaign, with a setup form, project controls, results tables, structure previews, and downloads. Read the BindCraft2 announcement for the background and what has changed from BindCraft.
BindCraft2 is free to use on Ariax Bio apart from compute costs. Academic and commercial customers do not need a separate BindCraft2 commercial license to run projects on Ariax.
Start with a small campaign
- Choose a design format in the sidebar or New Project, then select BindCraft2 where an engine choice is offered.
- Upload a PDB or mmCIF target, or search the Protein Data Bank from the setup page. Select the chains you want the binder to recognize.
- Keep the format's default design settings for your first run. Add hotspot residues if you have a specific binding site in mind.
- The form starts with 10 final designs. Set Maximum Trajectories if you want to cap the number of attempts in a pilot; leaving it blank does not impose an attempt limit.
- Review GPU preferences and the estimated hourly cost. Name the project, then select Start BindCraft2.
An accepted design is a candidate that passed the campaign's computational filters. One design attempt can fail before producing an accepted candidate, so requesting 10 final designs does not mean the engine will run only 10 attempts. An attempt limit bounds the search, not its total cost or duration.
Choose a format
| Format | Starting point and default length |
|---|---|
| Fab | Bundled antibody-fragment scaffold, including variable and constant domains of the heavy and light chains. |
| scFv | Bundled heavy- and light-chain variable-domain scaffold. BC2 designs two chains; it does not design the connecting linker. |
| VHH | Bundled single-domain antibody scaffold. |
| Large Binder | De novo binder; default range 250–600 residues. |
| Miniprotein | De novo binder; default range 60–180 residues. |
| Ankyrin Repeat Protein (ARP) | Bundled ankyrin-repeat scaffold. Listed as Ankyrin Repeat in navigation. |
| Peptide | Linear peptide; default range 12–25 residues. |
| Cyclic Peptide | Peptide intended for head-to-tail cyclization; default range 6–16 residues. |
Length ranges are inclusive. Set the minimum and maximum to the same value for a fixed length. Scaffolded formats derive their lengths from the scaffold and editable regions rather than the de novo length fields.
Homo-oligomer and Multidomain are specialized choices within BindCraft2 setup. Homo-oligomers use identical binder copies, with lengths specified per copy; multidomain designs place multiple domains in one chain. They are not separate engines. Helicon design remains a BoltzGen workflow.
For a custom scaffold, choose Custom scaffold, upload its PDB/mmCIF file, and specify Editable Residues. The field supports the engine's residue-selection syntax, including variable-length loop edits such as A52-57(5-7). Keep bundled editable-region defaults unless you have a reason to change them. Review the resulting chain sequences carefully before preparing antibody constructs for synthesis.
Prepare targets and binding sites
The first target must be a PDB or mmCIF structure. Standalone sequence-only projects are not yet supported in Ariax. Additional targets can use structures or FASTA files; for FASTA, select the intended record. A sequence target has no structure preview or structure-based hotspot picker.
Use the target selector to move between uploaded targets. Give each a recognizable name, select its chains, and review the structure preview. You can use Prep Inputs to inspect and trim a structure before uploading it. Keep enough structural context to represent the binding site, and check the proposed pose against the full biological assembly before selecting designs for experiments.
- Hotspots identify residues you want the binder to engage. Use input residue numbering, for example
A54,A56,B12-16. Unprefixed numbers refer to the first selected chain. You can also select residues in the structure viewer. - Coldspots identify regions you want the binder to avoid. They are an optional targeting setting, not a guarantee of selectivity in an experiment.
- Objective: Target promotes binding to that input. Multiple positive targets ask the same binder to work across the supplied targets or states.
- Objective: Detarget discourages binding to a supplied off-target. Keep at least one positive target and choose off-targets that answer a meaningful biological question.
- Weight controls a target's relative contribution to the design objective. Leave the default unless deliberately balancing a multi-target experiment.
Additional target options include FASTA cropping and detargeting controls. Open these only when relevant; the form checks whether they are compatible with the selected inputs and objectives.
Defaults and optional settings
BindCraft2 Design Settings contains the main decisions: format, scaffold or binder length, requested final designs, and optional attempt limit. The default presets set the optimization and filtering behavior for that format.
Optional Design Objectives exposes Forced targeting, Humanize, Protease stability, Disulfide staple, Mixed topology, Termini together, Accessible termini, Initial guess, and Big bang. Induced fit and Fold switching compare free and bound conformations. These objectives have compatibility restrictions; some require one target, exclude detargeting, or cannot be combined with a scaffold. Let the setup form's validation guide the supported combinations.
These settings optimize computational proxies. For example, Humanize does not establish that a design will be non-immunogenic, and a protease-stability objective does not establish experimental stability. Use only the properties your experiment needs.
Advanced Settings contains optional optimization, redesign, validation, output, and metric-filter overrides. Blank fields retain the engine's defaults; zero is an explicit value, not another way to request the default. Changing a threshold can change which candidates are accepted. A campaign with easier filters should not be compared directly with a stricter campaign on accepted-design count alone.
BindCraft2 can adapt its search as a campaign runs. The trajectory CSV's autotuned field records per-attempt changes, including changes that make a difficult search more permissive. Review those records when comparing campaigns or selecting candidates. The recorded campaign settings and individual trajectory records answer different questions: what you requested, and how a particular attempt ran.
Before launching, open Submission Summary to review the scientific settings and explicit overrides. After launch, Project Settings → Additional settings → Recorded settings provides the project's recorded configuration. Use Clone & Reuse to start a separate experiment with revised settings; editing GPU preferences does not change the scientific design task.
GPU preferences and costs
Choose Performance or Cost to rank eligible GPU offers. Allowed GPUs limits the classes Ariax may use; choices without enough memory for the current campaign are excluded. Larger structures, longer binders, extra targets, and additional binder chains can increase memory requirements.
Turbo Mode allows a campaign to use 2, 4, or 8 GPUs when a matching provider allocation is available. BindCraft2 assigns native workers across the visible devices automatically. Turbo can shorten elapsed time, but the combined hourly cost is higher when more resources run. The displayed hourly estimate is not a fixed price for the completed campaign. Scientific rejection rates and provider availability also affect how long a run takes.
If no compatible resource can be allocated, the project pauses with an explanation. Review GPU preferences, available credit, and the displayed reason before restarting. Do not loosen scientific settings merely to clear a compute-selection problem.
See Billing & Credits for account funding and usage charges.
Monitor and control a project
The project page uses the familiar Project Settings, Project Status, Resource Usage, and Results sections. Accepted-design progress measures progress toward the requested count; it is not an estimate of time remaining.
Project status is running, paused, aborted, failed, completed, or deleted. A latest job can separately be pending while waiting to start. A Campaign phase, such as planning or designing, describes what the engine is doing; it is not a separate project status.
- Pause asks the running campaign to stop and save its progress. Allow time for results to finish saving.
- Restart resumes a paused project from available saved progress, using its recorded scientific configuration. Resolve the pause reason first—for example, add credit or adjust GPU preferences.
- Abort ends the campaign. Use Pause when you intend to resume it.
- Clone & Reuse opens a new setup form populated from the project, so you can change the experiment without changing the original record.
- Delete is available when the project is eligible for deletion. Download anything you need before deleting a project.
Provider interruptions can trigger recovery onto replacement compute. Work completed after the most recent saved checkpoint may need to be repeated. Check the project message and Resource Usage for the current state; avoid submitting another copy of the campaign while recovery or final saving is in progress.
Read results and CSV files
The Results tabs show three stages of the design process:
| Tab | Native CSV | What it tells you |
|---|---|---|
| Final Results | 3_Ranked/!_Ranked.csv |
Accepted designs, ranked for review. Start here when choosing candidates. |
| Refolded Candidates | 2_Refolded/!_Refolded.csv |
Redesigned sequences and their validation outcomes, including rejections. |
| Trajectories | 1_Trajectories/!_Trajectories.csv |
Earlier design attempts, where they stopped, and per-attempt settings. |
The page reads these CSVs into paginated tables. Expand a design's name to inspect its sequences and recorded measurements. Where several structures are available, choose the relevant target complex or binder structure, then select View to open the structure viewer or download the file. Select Refresh Results to request the latest published results.
Each tab has Download CSV for the underlying table, including columns beyond the compact on-screen summary. A table can be empty before its stage has produced output. A completed search can also have no accepted designs if it reached its attempt limit without a candidate passing the filters.
Useful measurements include:
| Measurement | Interpretation |
|---|---|
i_pDAE |
BC2's standard interface-ranking score, on a 0–1 scale; higher is better. It is a distance-masked confidence measure, not binding affinity. |
i_pTM |
Predicted interface confidence, on a 0–1 scale; higher is better for a positive target. |
pLDDT |
Mean binder confidence in the CSV, on a 0–1 scale. Per-residue pLDDT stored in a predicted structure's B-factor field uses 0–100 instead. |
i_pAE |
Normalized interface prediction error; lower is better. Its scale differs from a PAE matrix reported in ångströms. |
failed_filters |
Criteria that rejected a candidate. A missing measurement is not the same as a score of zero. |
Binder_Sequence |
Designed amino-acid sequence; / separates binder chains. |
For multi-target campaigns, CSV metric cells can contain semicolon-separated values aligned with the targets column. Preserve empty entries when parsing the CSV, and do not average positive-target and detarget scores together. Use a CSV reader or spreadsheet import rather than splitting lines on commas: quoted fields can themselves contain commas.
Rank is not a probability of experimental success. Inspect the interface, target accessibility, glycans, membrane context, and intended assay geometry before choosing sequences for synthesis.
Files, archives, and logs
Project Files lets you browse Inputs and Results, download individual files, and preview supported structures. Preserve the CSVs and campaign_metadata.json alongside the structures so the shortlist remains connected to its settings and measurements.
Download Results Archive collects the published project results into one archive. Inputs and logs can be downloaded separately. The download dialog supports a browser download or a command/link for tools such as cURL, wget, and aria2c. If a signed link expires, reopen the dialog to get a fresh link. An archive may not be available until the campaign has saved and published its results.
The Logs panel displays the available campaign log and offers Download Logs. It is not limited to a 200-line preview. If the job has not started, there may be no log yet; use Load Logs or Refresh Logs to check again.
Troubleshooting
- The target will not load: check the file format, selected chains, and residue numbering. The first target must have a structure; a FASTA-only project cannot be launched yet.
- No designs have been accepted: check Trajectories and Refolded Candidates to see whether the search is still progressing or repeatedly failing a particular filter. Review the target and intended site before relaxing thresholds.
- The project is paused: read the reason, address credit or GPU eligibility issues as applicable, then use Restart. Wait for saving to finish if controls are temporarily disabled.
- The submission response was lost: open the dashboard and check whether the project was created before attempting another submission.
- A download is unavailable: refresh results or reopen the archive dialog. A result cannot be downloaded until it has been published by the running job.
For help, contact info@ariax.bio with the project ID and a description of what you expected. For other design approaches, see Project Types.