Evaluate Prot Param

Runs protein parameters evaluation on the provided batch of proteins, calculating various sequence and structure properties at specified pH values.

Quick Start

1. Connect a PDB batch to the node's input.
2. Specify a comma-separated list of pH values (e.g., 7,5.5,8).
3. Run the node to obtain a CSV table of protein parameters.

Setup Guide

1. Prepare Input Data

1. Generate or load a batch of protein structures in PDB format.
2. Ensure each PDB has a unique identifier.

2. Configure Node

1. Set the pH_list field to the desired pH values (comma-separated, e.g., 7,5.5,8).
2. Connect the PDB input.

3. Run Evaluation

1. Execute the node to compute parameters for each structure at each specified pH.
2. Download or inspect the resulting CSV output.

Basic Usage

Batch Protein Parameter Evaluation

• Evaluate isoelectric point, charge, and other sequence/structure properties for multiple proteins at different pH values.
• Use in workflows to compare designed proteins or validate generated structures.

Configuration

Required Inputs

Field	Description	Type	Example
pdb	Structures to evaluate.	PDB	{"design_0": "...PDB..."}
pH_list	Comma-separated list of float pHs to calculate protein charge.	STRING	7,5.5,8

Optional Inputs

None

Outputs

Field	Description	Example
score.csv	Scores of the foldings (various protein/sequence params)	CSV

Best Practices

Input Preparation

• Use unique IDs for each PDB to avoid confusion in batch outputs.
• Provide realistic pH values relevant to your experimental or biological context.

Workflow Integration

• Combine with diversity or functional evaluation nodes for comprehensive protein assessment.
• Use in automated pipelines to benchmark multiple designs.

Troubleshooting

Common Issues

• Empty or malformed PDB input: Ensure all PDBs are valid and properly formatted.
• Incorrect pH format: Use comma-separated floats (e.g., 7,5.5), not lists or other delimiters.

Need Help?

• Contact support for further assistance.