Scoring functions for protein structure prediction
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Date
2008
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Abstract
The following sections are included:
Introduction
Structure and Components of Scoring Functions
Contact Scoring Functions
Distance-dependent Scoring Functions
Accessible Surface Scoring Functions
Combined Scoring Functions
How is a Scoring Function Derived?
Selection of Source Experimental Data
Reference Systems
How is a Scoring Function Used?
Classical Overall Score Calculation
Sequence space reference frame
Structure space reference frame
Classical Detailed Score Calculation
Variations on Score Calculations
Typical Applications of Scoring Functions in Protein Structure Prediction
Fold Assessment
Model Ranking
Error Detection
Folding and Molecular Simulations
Other Applications of Scoring Functions
Future Outlook
Reference Systems and Atom Type Definitions
Solvation Models
Evolutionary Information
Multivariate Scoring Functions
Acknowledgements
References