User Guide

How to Use AlphaSuite

Last updated: 11 April 2026

AlphaSuite is designed for researchers who want to move quickly from a protein identifier to an interpretable 3D structure. You do not need to be a structural biology specialist to use it well, but it helps to be comfortable with proteins, residues, domains, motifs, and PDB / UniProt identifiers.

Getting Started Reading the Workspace Residue Search Common Questions Example Workflows

1. Search

Enter a UniProt or PDB ID

Use a UniProt accession such as P00533 when you care about the whole protein, or a PDB accession such as 6RAW when you want a specific experimental structure.

2. Inspect

Read the structure in context

Use the 3D viewer, sequence map, and annotation cards together. AlphaSuite is most useful when you compare what is annotated in UniProt with what is actually present in the current structure.

3. Compare

Switch between structures

If a motif or domain looks missing, check Other Available Structures. Experimental PDBs often capture only part of a protein, while AlphaFold can sometimes provide fuller coverage.

1. Reading the Workspace

Monomer shows the primary annotated chain. Use this when you want domain, motif, and residue-level interpretation for one protein target.
Complex shows the full assembly, including partners and ligands. Use this when you care about interaction context more than motif-level detail.
Other Available Structures lets you switch between experimental PDB entries and AlphaFold models when available.
Domains & Motifs lists the annotations AlphaSuite mapped onto the current structure. A region may be biologically real but still absent from the current PDB if that structure does not resolve it.
Sequence Map shows where domains and motifs fall across the full UniProt sequence, not just the residues visible in the current experimental structure.

2. What AlphaSuite Is Actually Showing

AlphaSuite combines third-party biological annotation with structure mapping. That means one annotation can be true for the protein overall but still not be visible in a particular PDB.
If AlphaFold is available, it can be useful for fuller sequence coverage. If AlphaFold is not available, AlphaSuite will tell you and you should interpret the current experimental structure as partial coverage.
Residue numbering in your question may be UniProt numbering, while residues in a PDB file can use author numbering. AlphaSuite handles the mapping, but this is why a residue can exist biologically even when it is not present in the rendered model.

3. Residue Search

The residue search bar is there to help answer practical research questions quickly. It accepts single positions, lists, ranges, and mutation-style inputs.

75 focuses residue 75.
75, 69, 125 highlights multiple positions together.
220-285 focuses a residue range.
Gly175Asp is treated as residue 175.

When you search, AlphaSuite tries to do two things at once: show the residues in sequence space and focus them in 3D if the current structure actually contains them. If a residue is not resolved in the current structure, AlphaSuite can still show where it belongs in the sequence even though it cannot place it in 3D.

4. Downloads

The .pml download is for PyMOL. AlphaSuite exports the current annotation logic and colouring into a PyMOL script so you can continue analysis, presentation, or figure-making outside the browser.

5. Common Questions

Why can’t I see all domains in this PDB? Because the PDB may only resolve part of the protein. The sequence map is still showing the full UniProt annotation context.
Why does AlphaSuite say something is outside this PDB? Because the annotation belongs to the protein, but the current structure does not contain those residues in resolved 3D coordinates.
Why is AlphaFold missing? Not every protein currently has an AlphaFold DB predicted structure available through the upstream source.
Why do structures differ? Different PDBs can represent different constructs, assemblies, truncations, liganded states, or experimental conditions.
What does Colour By mean? Both preserves the full AlphaSuite view, while Domains and Motifs simplify the colour logic so overlapping annotations are easier to read.

6. Example Workflows

Find which feature a mutation sits in

Search: 175 or Gly175Asp

Use residue search to focus the site, then inspect the annotation cards and sequence map to see whether the residue sits inside a known domain or motif. If the residue is not resolved in the current PDB, switch structures.

Check whether several residues cluster in 3D

Search: 75, 69, 125

This highlights multiple residues together and focuses them in the same structural view, which helps answer whether sequence-distant residues might be spatially close.

Inspect a putative binding segment

Search: 220-285

Use a range search to focus a suspected binding region, then compare Domain view, Motif view, and the surrounding annotation cards. If the segment is only partially present, try another structure.

Decide whether to use a PDB or AlphaFold model

Start with a UniProt ID, then compare Other Available Structures

Use experimental PDBs when you care about observed structure, interfaces, or ligands. Use AlphaFold when you need broader sequence coverage and the predicted model is available.

7. Best Practices

Start with the structure you care about most, but always sanity-check coverage using the sequence map.
Use Domains mode when the map feels visually crowded and you want the cleaner structural hierarchy first.
Use Motifs mode when the biologically interesting question is about a small annotated site inside a larger domain.
If a result looks wrong, ask whether it is a mapping issue or simply a structure-coverage issue. In AlphaSuite, that distinction matters a lot.