UniDesign

Introduction

UniDesign is a computational framework for protein design, targeting a diversity of protein design and engineering tasks, and it can also be used for protein structure modeling and scoring. UniDesign is extended mainly from the EvoEF2 protein design program with the evolutionary feature taken from EvoDesign, but it has many new features. More details can be found in manual.docx within this package.

Fig 1. UniDesign's capacities and its workflow for enzyme design

Main Applications

Protein Design

• Design monomer protein
• Design protein-protein interaction
• Design protein-ligand interaction
• Design protein-nucleic acid interaction
• Design enzymes

All protein design tasks are conducted with UniDesign command ProteinDesign with specific options. See manual.docx for details and examples.

Protein Structure Modeling

• Protein side-chain packing (command ProteinDesign with option --wildtype)
• Repair incomplete protein sidechains (command RepairStructure)
• Protein minimization to remove sidechain clashes (command Minimize)
• Build mutant structural models (command BuildMutant)
• Add polar hydrogen atoms (command AddPolarHydrogen)
• Optimize hydrogen atom's position (command OptimizeHydrogen)

Protein Scoring

• Compute protein stability (command ComputeStability)
• Compute protein interchain binding interaction (command ComputeBinding)

Installation, Usage and Tutorial

Please refer to the manual.docx for details.

Contact

For suggestions, please contact xiaoqiah@umich.edu or xiaoqiah@outlook.com.

References

Huang, X., Zhou, J., Yang, D., Zhang, J., Xia, X., Chen, Y. E., and Xu, J. Decoding CRISPR–Cas PAM recognition with UniDesign. Briefings in Bioinformatics. 2023, 24(3):bbad133. doi: 10.1093/bib/bbad133

Huang, X., Sun, Y., Osawa, Y., Chen, Y. E., and Zhang, H. Computational Redesign of Cytochrome P450 CYP102A1 for Highly Stereoselective Omeprazole Hydroxylation by UniDesign. Journal of Biological Chemistry. 2023, 299(8):105050.