How to Design and Evaluate Protein Sequences

1. Function Description

Enter a protein backbone structure or PDB ID, and the system can design new amino acid sequences based on ProteinMPNN, helping users obtain candidate protein sequences for downstream structure prediction, stability evaluation, and protein optimization research.

2. Case Demonstration

2.1 Four-Helix Bundle Protein Sequence Design and Stability Validation Using ProteinMPNN

2.1.1 Input Requirements

Given a four-helix bundle backbone structure (PDB: 1JMB), redesign the amino acid sequence using ProteinMPNN to improve thermal stability

 Reference Link

  After submission, the following steps will be performed automatically:

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  • Load the ProteinMPNN skil

  • Retrieve the 1JMB structure before running the sequence redesign

  • Reply with “yes” to submit the sequence design task

  • The system will then provide top 5 candidates

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2.1.2 Key Design Insights

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2.1.3 Project Report

After all tasks are completed, the agent will generate a project report based on the execution results for users’ downstream experimental reference.

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