Structure Prediction overview
Fetch a known structure by UniProt ID or predict one from sequence, read its confidence metrics before you trust it, then protonate it for electrostatics.
Before you can dock a molecule, find a binding site, or reason about a mutation, you need a 3D structure. This section gets you one — fetch a known structure or predict a novel or engineered sequence — plus the tools to judge and analyze it. Structure is the entry point for most target-side workflows.
Availability
These tools are metered by credits and gated by your plan — plans set your monthly credits, available model families, and which modal-app tools you can run. See Plans & tiers.
What you can achieve here
- Get a 3D structure — fetch a known one, or predict a novel/engineered sequence
- Find and rank druggable binding pockets
- Assess model confidence before you trust it downstream
- Compare a sequence against known structures and homologs
For which tool fits each, see What you can achieve.
Tools in this section
| Tool | What it does |
|---|---|
| ESMFold on the platform | Predict protein structures with ESMFold and interpret confidence metrics. |
| AlphaFold on the platform | Fetch pre-computed AlphaFold structures from the EBI AlphaFold Database by UniProt ID. |
| ESM-3 on the platform | Embed a sequence with ESM-3 for alignment-free similarity, zero-shot function prediction and clustering — per-residue and per-sequence vectors, not a… |
| PDB Search & Download on the platform | Search and retrieve protein structures from the RCSB Protein Data Bank. |
| PDB2PQR | Assign protonation states and prepare proteins for electrostatics calculations. |
| BLAST | Align a nucleotide or protein query against NCBI databases and score the hits, locally or remotely from a job, then fold the top hit with ESMFold. |
Recipes using these tools
Read next
Reading a result against the bench
How predicted structures compare to experimental ones, with citations per tool.
What you can achieve
The outcomes these tools deliver — and which to pick when several do the same thing.
Which tool?
Match a scientific goal to a tool across every domain.
Concept clusters
How tools, jobs, and results fit together.
Workflows
Guided pipelines and copy-and-adapt prompt recipes for common goals.
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