---
title: "Structure Prediction overview"
description: "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."
tags:
  - section
  - structure-prediction
generated: true
---

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](/docs/plans-and-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](/docs/capabilities).

## Tools in this section

| Tool | What it does |
|---|---|
| [ESMFold on the platform](/docs/esmfold) | Predict protein structures with ESMFold and interpret confidence metrics. |
| [AlphaFold on the platform](/docs/alphafold) | Fetch pre-computed AlphaFold structures from the EBI AlphaFold Database by UniProt ID. |
| [ESM-3 on the platform](/docs/esm3) | 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](/docs/pdb) | Search and retrieve protein structures from the RCSB Protein Data Bank. |
| [PDB2PQR](/docs/pdb2pqr) | Assign protonation states and prepare proteins for electrostatics calculations. |
| [BLAST](/docs/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