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Evaluation of protein models by atomic solvation preference.

L Holm¹, C Sander

¹European Molecular Biology Laboratory, Heidelberg, Germany.

Journal of Molecular Biology

|May 5, 1992

Summary

This study introduces a solvent contact model to predict protein structure stability. The model accurately distinguishes correct protein folds from incorrect ones, aiding in protein design and simulations.

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Area of Science:

Computational biology
Structural bioinformatics
Protein folding

Background:

Protein stability is crucial for function and depends on solvent interactions.
Accurate prediction of protein structure is essential for understanding biological processes.

Purpose of the Study:

To develop and test a "solvent contact model" for predicting protein structure.
To evaluate the model's ability to discriminate correct protein folds from incorrect ones.

Main Methods:

Derived atomic solvation preference parameters from known protein structures.
Employed Monte Carlo simulations with simulated annealing to optimize side-chain conformations.
Tested discrimination ability on native-like vs. non-native-like protein models.

Main Results:

The solvent contact model clearly distinguished between correct and misfolded protein structures.
The method proved effective for entire protein models, with some success in identifying local errors.
Computationally efficient compared to surface area calculation methods.

Conclusions:

Solvation preference is a valuable metric for assessing protein model accuracy.
The model serves as a fast diagnostic tool for protein model building, folding simulations, and protein design.

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