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

 参考链接

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

  After submission, the following steps will be performed automatically:

• Retrieve the PDB structure (1MBG) and generate a visualized structural model

• Perform a pre-check of ProteinMPNN design parameters

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

•   The system will then return the execution results and provide downloadable FASTA files.

2.1.2 Result Validation

Provide downstream workflow options

Perform stability validation and structure validation separately.

1. Fold validation

• During execution, parameter-related errors may occasionally cause prediction failures.The agent will automatically diagnose the issue, adjust the parameters, and rerun the prediction task.

• Predicted structures can be viewed by clicking the card labeled “View Predicted 3D Structure”.

• The predicted structure PDB files will be automatically saved to My Cloud Drive, where they can also be downloaded directly from the interface or cloud storage.

• Rosetta

  • The system will display the preset parameters for review.

  • Users should manually confirm and submit the Rosetta calculation task.

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.