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Updated: May 29, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates.
Stewart E Moughon1, Ram Samudrala
1Department of Microbiology, University of Washington, Box 357735, Seattle, Washington 98195-7242, USA. wtec@u.washington.edu
BMC Bioinformatics
|September 17, 2011
Summary
A new scoring function, LoCo, accurately predicts protein structures by analyzing residue interactions. This fast and simple method significantly outperforms existing functions, aiding in protein structure prediction and design.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Biophysics
Background:
- Accurate low-resolution scoring functions are crucial for identifying native-like protein main chain conformations.
- Early methods used simple distance-based potentials, while newer approaches incorporate amino acid relative orientations for improved performance.
Purpose of the Study:
- To develop a novel, knowledge-based scoring function for protein structure prediction.
- To enhance the accuracy and efficiency of identifying correct protein main chain conformations.
Main Methods:
- Developed LoCo, a scoring function using a local coordinate system based on main chain N, Cα, and C atom positions.
- Trained and optimized LoCo on experimentally determined structures and modeled structures (decoys), ensuring no overlap with test data.
Main Results:
- LoCo outperformed 29 other main chain functions on 77 decoy sets, achieving superior Cα RMSD rank for the best-scoring decoy (p < 0.05 for 26 functions).
- The function demonstrated high speed, averaging less than 6 microseconds per residue for interaction and scoring on standard hardware.
Conclusions:
- LoCo offers an exceptional combination of accuracy, speed, and simplicity for protein structure prediction.
- Potential applications extend to protein-protein interactions and protein design.
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