---
title: P2Rank inputs and parameters
description: >-
  PDB formats, model selection, and visualization options for
  P2Rank pocket prediction.
tags:
  - p2rank
  - inputs
---

You provide a protein 3D structure — a PDB ID, an uploaded file, or a structure from a previous job. The one choice that most affects the result is the model variant: use `default` for experimental crystal structures and `alphafold` for ESMFold or AlphaFold predictions, so pocket scoring accounts for prediction uncertainty.

## Webapp input methods

The .bloom* webapp provides several input methods for P2Rank pocket prediction.

## Input type selection

| Input Type | Description | Example |
|------------|-------------|---------|
| **PDB ID or UniProt ID** (`uniprot_id`) | A single field that accepts either — the tool auto-detects a 4-character PDB ID vs. a UniProt accession and fetches the structure | `6LU7`, `1M17`, `4HJO`, or `P00533` |
| **PDB content** (`pdb_content`) | Paste or upload PDB file content directly | Upload `protein.pdb` |
| **From previous job** | Import from ESMFold, AlphaFold, or PDB search — carried into `pdb_content` or `uniprot_id` the same way | Select from completed jobs |

There's no separate S3-URI parameter — a stored structure from a previous job is read and passed as `pdb_content`.

## Structure requirements

### PDB format
- **ATOM records**: Standard PDB format with all heavy atom coordinates
- **Chain identifiers**: Multi-chain structures must have unique chain IDs (A, B, C, etc.)
- **Standard residues**: 20 canonical amino acids; non-standard residues (modified AA, ligands) are ignored
- **Coordinates**: All coordinates in angstroms with reasonable B-factors

### Quality requirements
- **Resolution**: Best results with <3.0 angstrom resolution; >4.0 angstrom resolution may produce unreliable pocket predictions
- **Completeness**: Missing heavy atoms in the binding region reduce prediction accuracy; rebuild missing side chains if possible
- **Alternate conformations**: Only the A conformation is used; remove alternate conformers for clarity
- **Water molecules**: Crystallographic waters are ignored; P2Rank uses the protein surface only

### Structure preprocessing
- **Ligand removal**: Existing ligands in the PDB are automatically removed before prediction (P2Rank predicts from apo structure)
- **Hydrogen removal**: Hydrogen atoms are not used and are removed if present
- **Multi-model PDB**: Only the first MODEL record is used (relevant for NMR ensembles)
- **HETATM records**: Non-standard residues and small molecules are excluded from the analysis

## Model variant selection

| Model | Description | Training Data | Best For |
|-------|-------------|---------------|----------|
| **default** | Standard random forest model | Experimental PDB structures with bound ligands | General-purpose pocket prediction on experimental structures |
| **alphafold** | Adapted for predicted structures | AlphaFold and ESMFold predictions | Structures from ESMFold, AlphaFold, or other prediction methods |

### Choosing a model variant
- **default**: Use for experimental crystal structures from the PDB; best general performance
- **alphafold**: Use for ESMFold or AlphaFold predicted structures; accounts for lower accuracy of predicted models, especially in loop regions

## Prediction parameters

These are the actual parameters this tool accepts:

| Parameter | Type | Default | Description |
|-----------|------|---------|-------------|
| **uniprot_id** | string | - | PDB ID (4-char) or UniProt accession — auto-detected. Provide this OR `pdb_content` |
| **pdb_content** | string | - | PDB file content, or a structure Ivy already fetched from the PDB in this chat |
| **model** | string | `default` | Model variant (`default`, `alphafold`) |
| **max_pockets** | integer | 10 | Maximum number of pockets to report (1-50) |
| **visualization** | boolean | true | Generate PyMOL visualization script |

There's no chain-filtering parameter, no minimum pocket score/size threshold, and no color-scheme or surface-type option — P2Rank analyzes the full structure as submitted, and druggability/rank are read from the returned pocket table rather than set as an input filter.

## Previous job integration

### Compatible tools
- **ESMFold**: Predicted protein structures (use alphafold model variant)
- **AlphaFold DB**: Pre-computed structure predictions
- **PDB Search**: Experimental structures from RCSB PDB
- **PDB2PQR**: Protonated and charge-assigned structures

### Data handling
- **Automatic PDB extraction**: .bloom* extracts PDB content from various job output formats
- **Chain identification**: Chain information is parsed and displayed for reference (there's no chain-filter parameter — all chains in the submitted structure are analyzed together)
- **Provenance tracking**: Maintains connection to the original structure source

## Read next