---
title: ESMFold inputs and parameters
description: Prepare sequences and configure ESMFold predictions in .bloom* platform.
---

You provide a single-chain protein sequence — pasted directly, fetched by UniProt ID, or imported from a previous job. The one input that most affects your result is the sequence itself: keep it within the 50–500 residue optimal range and free of non-standard residues, since length and composition drive both runtime and confidence.

## Webapp input methods

The .bloom* webapp provides three input methods for ESMFold protein structure prediction:

## Input type selection

| Input Type | Description | Example |
|------------|-------------|---------|
| **Protein Sequence** | Direct amino acid sequence entry | `MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTK...` |
| **UniProt ID** | Automatic sequence fetch from UniProt | `P68871`, `Q9Y261` |
| **From Previous Job** | Import from BLAST, other folding jobs | Select from job outputs |

## Protein sequence input (default)

- **Format**: Raw amino acid sequence using single-letter codes
- **Validation**: Real-time checking for invalid characters
- **Placeholder**: "Enter protein sequence..."
- **Multiline**: 4-row text area for longer sequences

## UniProt ID input

- **Format**: UniProt accession codes (e.g., `P00533`, `P68871`)
- **Auto-fetch**: Automatic sequence retrieval from UniProt database
- **Validation**: Real-time format checking

## From previous job

- **Job Output Selector**: Browse completed jobs with protein sequence outputs
- **Compatible tools**: BLAST sequence searches, other protein analysis jobs
- **Data type**: Requires `fasta` data type output
- **SMILES extraction**: Automatic sequence extraction from job results

## Sequence requirements

ESMFold accepts single-chain protein sequences containing only the 20 standard amino acids. Key requirements:

- **Standard amino acids only**: The model only accepts the canonical 20 residues (ACDEFGHIKLMNPQRSTVWY)
- **No modified residues**: Selenocysteine (U), pyrrolysine (O), and ambiguous codes (B, J, X, Z) are not supported
- **Single chain**: Multi-chain complexes and heteromers are not directly supported
- **Length limits**: Optimal performance for sequences between 50-500 residues; sequences up to 2,500 residues are accepted but may have reduced confidence in some regions past ~1,000 residues

## Direct sequence entry

### Plain amino acid sequence
- **Format**: Raw amino acid sequence using single-letter codes
- **Validation**: Real-time checking for invalid characters
- **Length limits**: 10-2,500 residues (optimal: 50-500)
- **Case sensitivity**: Automatically converted to uppercase

### FASTA format
- **Headers**: Descriptive names for result tracking
- **Multiple sequences**: One sequence per FASTA entry
- **Header format**: `>identifier description` (e.g., `>P12345 Hemoglobin beta chain`)
- **Length limits**: Same as plain sequence (10-2,500 residues total)

### Sequence properties display
- **Length**: Total amino acid count
- **Molecular weight**: Calculated from sequence composition
- **Isoelectric point**: Theoretical pI based on amino acid charges
- **Composition**: Amino acid frequency analysis

## UniProt integration

### Accession lookup
- **Format**: UniProt accession codes (e.g., P68871, Q9Y261)
- **Validation**: Real-time checking against UniProt database
- **Auto-fetch**: Automatic sequence retrieval and metadata loading
- **Isoforms**: Selection of alternative splice variants when available

### Metadata integration
- **Protein names**: Full protein names and aliases
- **Organism**: Source organism information
- **Function**: Known or predicted protein function
- **Domains**: Annotated functional domains and features

## Previous job integration

### Compatible tools
- **BLAST**: Sequence search results with hit sequences
- **Sequence analysis**: Extracted or processed sequences
- **Other folding jobs**: Previously predicted structures (sequence extraction)

### File handling
- **Multi-sequence files**: Automatic parsing and selection
- **Format conversion**: Handling various sequence file formats
- **Provenance tracking**: Maintains connection to original data source

## Sequence validation and preprocessing

### Character validation
- **Standard amino acids only**: ACDEFGHIKLMNPQRSTVWY
- **Exclusion of ambiguous codes**: B, J, O, U, X, Z not allowed
- **Special characters**: Automatic removal of whitespace, numbers, and punctuation

### Sequence cleaning
- **Whitespace removal**: All spaces, tabs, and line breaks stripped
- **Number removal**: Position numbers and other numeric characters
- **Case normalization**: Conversion to uppercase for consistency
- **Non-amino filtering**: Removal of any non-amino acid characters

### Length optimization
- **Chunking**: Automatic splitting for very long sequences (>500 residues)
- **Domain splitting**: Manual splitting at low-complexity regions
- **Memory considerations**: Guidance for optimal sequence lengths

## Webapp parameters

### Personalized settings toggle

- **Use Personalized Settings**: Checkbox to enable project-specific configuration
- Loads settings from Supabase when enabled
- Settings are keyed by `esmfold_settings` per project

### Advanced settings (via settings panel)

Click **"Advanced settings…"** to access additional parameters:

**Prediction quality:**
- **Num Recycles**: Refinement iterations for structure prediction
  - Higher values improve accuracy but increase runtime
  - Configurable via global tool settings
- **Chunk Size**: Sequence segmentation for long proteins
  - Automatic optimization based on sequence length
  - Manual override available for specific requirements

### Submit button

- **Label**: "Fold Protein"
- **Disabled when**: No sequence entered (manual) or no job output selected (previous job)
- **Keyboard shortcut**: Enter to submit (via EnterSubmitContainer)

### Job status and ETA

- **EstimatedTimeWidget**: Shows estimated processing time for ESMFold jobs
- **Live ETA**: Real-time completion estimate during job processing
- **Progress tracking**: Phase-based progress indication

## Output options

- **PAE matrices**: Predicted aligned error data (default: enabled)
- **Confidence scores**: Per-residue pLDDT values (default: enabled)
- **Secondary structure**: Predicted helices and sheets

## Batch processing strategies

### Single sequence jobs
- **Recommended approach**: One sequence per job for predictable results
- **Runtime consistency**: More reliable completion times
- **Error isolation**: Issues affect only individual sequences

### Multi-sequence batches
- **Short sequences**: Peptides and small proteins (<100 residues)
- **Aggregate limits**: Total length <500 residues recommended
- **Monitoring**: Track individual sequence completion status

### High-throughput workflows
- **Queue management**: .bloom*'s job queuing system handles multiple submissions
- **Progress tracking**: Real-time status across all batch jobs
- **Result aggregation**: Tools for comparing multiple predictions

## File preparation guidelines

### FASTA formatting best practices
- **Clear identifiers**: Use meaningful names for result mapping
- **Standard format**: `>identifier|description|additional_info`
- **Length limits**: Keep headers under 200 characters
- **Special characters**: Avoid pipes, commas, and other delimiters in headers

### Sequence quality checks
- **Reading frame**: Ensure correct translation from DNA if applicable
- **Start/stop codons**: Proper handling of translation initiation/termination
- **Splice variants**: Consideration of alternative splicing effects
- **Post-translational modifications**: Awareness of potential PTM sites

### Pre-submission validation
- **External tools**: Use sequence validation software if available
- **Homology checking**: BLAST against known structures for reference
- **Domain identification**: Check for known structural domains
- **Unusual compositions**: Flag sequences with extreme amino acid biases

## Error handling and troubleshooting

### Common input errors
- **Invalid characters**: Non-standard amino acid codes
- **Length violations**: Sequences outside supported range
- **Format issues**: Malformed FASTA or corrupted files

### Validation feedback
- **Real-time checking**: Immediate error highlighting in webapp
- **Actionable messages**: Specific guidance for fixing issues
- **Suggestion system**: Automatic recommendations for common problems

### Recovery strategies
- **Sequence cleaning**: Tools for removing problematic characters
- **Format conversion**: Utilities for fixing file format issues
- **Splitting**: Breaking long sequences into manageable chunks

## Read next