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Estimates for the potential accuracy required in realistic protein folding simulations and structure recognition
1Biophysics Program, Brandeis University, Waltham, MA 02254, USA.
Folding & Design
|January 1, 1997
Summary
Protein folding simulations require less accuracy than previously thought. Even with significant energy errors, computational models can still predict protein structures effectively.
Area of Science:
- Computational Biology
- Biophysics
- Protein Folding
Background:
- Previous work established theoretical considerations for protein folding simulation accuracy.
- This study integrates theoretical formalism with the law of corresponding states.
Purpose of the Study:
- To estimate the required potential accuracy for computational studies of a small helical protein.
- To determine the permissible energy error for protein structure recognition and ab initio folding simulations.
Main Methods:
- Combined theoretical formalism with the law of corresponding states.
- Utilized lattice model simulations for analysis.
Main Results:
- An error of +/- 330 cal mol-1 is acceptable for structure recognition, maintaining the native conformation as the global minimum.
- For ab initio folding simulations, permissible error varies with temperature, up to +/- 120 cal mol-1.
Conclusions:
- Potentials do not require extreme accuracy for computational utility.
- Current potentials may be too inaccurate for ab initio simulations but are nearing the limit for structure recognition.