Ariax.bio

Ariax.bio

Prepare Inputs

5. Prepare Inputs

New to structure preparation?
Check out our comprehensive Prep Inputs tutorial for a step-by-step walkthrough with screenshots and practical examples.

Before launching a protein design project, you need to prepare your target structure file and optionally select target hotspots. Traditionally, this requires specialized software like PyMOL or ChimeraX, which have steep learning curves. Ariax's Prep Inputs tool simplifies this entire workflow in your browser—completely free, with no files uploaded to our servers and all processing happening locally on your computer.

5.1 What is Prep Inputs?

Prep Inputs is a browser-based tool for preparing protein structures for computational design. It helps you:

  • Load structures from local files (PDB/CIF) or directly from RCSB
  • Trim structures by removing chains and residues to optimize compute efficiency
  • Visualize structures with multiple representation modes (cartoon, licorice, surface, electrostatic)
  • Analyze structures using B-factor coloring and secondary structure highlighting
  • Select hotspots manually or automatically via proximity detection
  • Export clean PDBs ready for BindCraft or other design platforms

No installation required. No data uploaded. Completely free to use—even if you run your design jobs elsewhere.

5.2 Accessing Prep Inputs

After creating your account, access Prep Inputs from:

  • The main navigation sidebar under "Plan"
  • Direct link: /plan/prep-inputs

5.3 Loading Target Structures

Prep Inputs supports two loading methods:

Upload Local Files

Select any PDB or CIF file from your computer. The tool automatically:

  • Parses both PDB and CIF formats
  • Extracts all chains and residue information
  • Converts everything to PDB format for export
  • Renders the structure in the 3D viewer

Search RCSB Database

Type a PDB ID (like "4GS7") or keyword search term. The tool:

  • Queries RCSB in real-time
  • Shows results with structure titles
  • Loads selected structures instantly
  • Displays all available chains

5.4 Trimming Chains and Residues

Chain Selection

Use checkboxes to select which chains to include in your final structure. Unchecked chains are removed from both the exported file and 3D visualization.

Residue Selection

Each chain displays residues as single-letter amino acid codes. You can:

  • Click individual residues to toggle visibility
  • Click and drag to select ranges
  • Hidden residues show strikethrough text
  • Missing residues appear as dots or gap markers

Size Guidance

A real-time status indicator tracks total residue count:

  • Green (< 400 residues): Well-sized for all Ariax GPUs
  • Yellow (400-800 residues): Requires powerful GPUs (H100+)
  • Red (> 800 residues): Not recommended—high risk of crashes

As discussed in our BindCraft tutorial, keeping structures under 300-400 amino acids ensures efficient design on most hardware.

5.5 Visualization Modes

Toggle between representation modes using icon buttons next to each chain:

Cartoon: Ribbon representation highlighting secondary structure—best for identifying domain boundaries

Licorice: All-atom stick representation—useful for examining interface contacts

Surface: Molecular surface colored by chain—reveals binding pockets and buried regions

Electrostatic Surface: Surface colored by charge distribution—helps identify charged patches and hydrophobic regions

Coloring Schemes

Chain: Each chain gets a distinct color for easy identification

B-factor: Colors by crystallographic temperature factors or AlphaFold pLDDT scores

  • AlphaFold structures: higher (blue) = greater confidence
  • Crystal structures: higher (red) = greater disorder
  • Helps identify disordered regions suitable for trimming

Secondary Structure: Colors helices, sheets, and coils distinctly—useful for identifying unstructured regions

5.6 Hotspot Selection

Define specific residues that BindCraft should preferentially target. While BindCraft can identify binding sites automatically, hotspots help focus designs on functional sites of interest.

Manual Selection

  1. Toggle "Select Hotspots" mode
  2. Click residues in the 3D viewer to add/remove from hotspot set
  3. Selected residues show yellow highlighting
  4. Hotspots format automatically for BindCraft (e.g., "A45,A50-55,B20")

Proximity-Based Selection

Automatically identify interface residues for targeting protein-protein interactions:

  1. Target Chain: Which chain(s) to search for interface residues
  2. Reference Chain: Which chain(s) or residues define the interface
  3. Radius: Distance threshold in angstroms (default 4.5 Å)
  4. Residues (optional): Specific residue ranges for proximity calculation

Click "Detect Interface Residues" to automatically select all qualifying hotspots. This is particularly useful for designing competitive inhibitors or interface binders.

5.7 Exporting Prepared Structures

Once trimming and hotspot selection are complete, choose your export option:

Download Trimmed PDB

Saves a clean PDB file with:

  • Only selected chains and residues
  • Proper formatting for any design platform
  • REMARK headers indicating selections

Compatible with BindCraft, RFdiffusion, ColabDesign, and other tools accepting PDB input.

Use in BindCraft

Seamlessly transfers to the BindCraft setup page:

  • Trimmed structure automatically loaded
  • Chain selections preserved
  • Hotspot configuration transferred
  • No copy-paste errors

Launch your design job immediately without manual file handling.

Next: 6. BindCraft Project Setup to configure and launch design jobs with your prepared structures.