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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
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Computational design of structured loops for new protein functions
Kale Kundert1,2, Tanja Kortemme1,2,3
1Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.
Biological Chemistry
|January 25, 2019
Summary
Designing functional proteins computationally remains a challenge, especially for structured loops. Advances in loop structure prediction offer a path towards computational loop design and routine protein function engineering.
Area of Science:
- Protein engineering
- Computational biology
- Biochemistry
Background:
- Functional proteins rely on precise geometries, energetics, and dynamics.
- Structured loops are key features of natural protein functional sites.
- Computational design of structured loops is a significant unsolved challenge.
Purpose of the Study:
- To review progress in computational loop design.
- To discuss leveraging loop structure prediction for inverse loop design.
- To enable routine design of protein function.
Main Methods:
- Review of current computational protein design strategies.
- Analysis of recent advances in protein loop structure prediction.
- Application of prediction methods to inverse design challenges.
Main Results:
- Structured loops are critical for protein function but difficult to design computationally.
- Loop structure prediction advancements provide new tools for design.
- Bridging prediction and design is essential for progress.
Conclusions:
- Harnessing loop structure prediction is key to advancing computational loop design.
- Overcoming challenges in loop design is a necessary step for engineering protein function.
- Future work should focus on integrating prediction and design methodologies.
Keywords:
Rosetta softwarebinding site designloop modelingpositioning functional residuesprotein designMore Related Videos
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