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Updated: Jun 25, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Solvent accessible surface area approximations for rapid and accurate protein structure prediction
Elizabeth Durham1, Brent Dorr, Nils Woetzel
1Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, Nashville, TN 37232-8725, USA.
Journal of Molecular Modeling
|February 24, 2009
Summary
Calculating solvent-accessible surface area (SASA) for protein folding is complex. A new "Neighbor Vector" algorithm offers an optimal balance of speed and accuracy for protein structure prediction.
Area of Science:
- Computational Biology
- Biophysics
- Structural Bioinformatics
Background:
- Protein folding is driven by the burial of hydrophobic amino acids.
- Solvent-accessible surface area (SASA) quantifies amino acid exposure but is computationally intensive.
- Accurate SASA calculation requires full-atom models and is not pair-wise decomposable.
Purpose of the Study:
- To develop computationally efficient approximations for SASA calculation.
- To create knowledge-based environment free energy potentials using SASA approximations.
- To assess the balance between speed and accuracy in protein structure prediction.
Main Methods:
- Introduction of four SASA approximations with varying complexity and accuracy.
- Development of knowledge-based environment free energy potentials.
- Assessment of algorithms for distinguishing correctly from incorrectly folded protein models.
Main Results:
- The
Conclusions:
- The
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