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Occluded molecular surface: analysis of protein packing
N Pattabiraman1, K B Ward, P J Fleming
1Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375-5000, USA.
Journal of Molecular Recognition : JMR
|November 1, 1995
Summary
We developed a new method to analyze protein structures by calculating atomic surface areas and interactions. This approach helps identify native-like protein models and assess molecular binding complementarity.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Biophysics
Background:
- Accurate assessment of protein structural models is crucial for understanding biological function.
- Existing methods may not fully capture the nuances of atomic packing and interactions within protein structures.
Purpose of the Study:
- To introduce a novel computational method for quantifying packing interactions in protein structural models.
- To develop a parameter diagnostic for native-like protein structures.
- To enable the assessment of molecular complementarity for interacting molecules.
Main Methods:
- Calculating interatomic occluded surface areas for each atom in a protein model.
- Extending surface normals to identify and quantify neighboring atom interactions.
- Normalizing surface areas by amino acid composition to derive the normalized protein surface ratio.
Main Results:
- The normalized protein surface ratio serves as a diagnostic for native-like protein structures.
- The method allows identification of residues in unusual packing environments.
- Explicit description of packing densities and environments for individual atoms is achieved.
Conclusions:
- This novel method provides a quantitative description of packing interactions in protein models.
- The normalized protein surface ratio is a valuable metric for assessing protein structural quality.
- The approach can be extended to estimate binding complementarity between molecules.