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Geometric versus topological clustering: an insight into conformation mapping
1Department of Chemical Physics, School of Chemistry, Tel Aviv University, Ramat Aviv, Israel. becker@sapphire.tau.ac.il
Proteins
|February 1, 1997
Summary
Geometric clustering of molecular conformations does not always align with energy basins. This study reveals that structural similarity is not a perfect indicator of energy landscape, impacting conformational analysis.
Area of Science:
- Computational Chemistry
- Molecular Modeling
- Biophysics
Background:
- Conformational analysis frequently employs clustering of molecular structures into geometric families.
- A common assumption is that these geometric families correspond to the energetic landscape of the potential energy surface.
Purpose of the Study:
- To investigate the correlation between structural similarity and energy basins in molecular systems.
- To assess the reliability of geometric 'family clustering' in reflecting the true energetic structure.
Main Methods:
- Topological mapping and principal coordinate projections were utilized.
- Analysis was applied to a small tetrapeptide system.
- Distances were measured in both dihedral angle and Cartesian spaces.
Main Results:
- A general correlation between energy basins and structural similarity was observed but found to be non-absolute.
- Geometric 'family clustering' did not consistently reflect underlying energy basins.
- The 'family tree' from geometric clustering was inconsistent with the 'disconnectivity' graph.
Conclusions:
- Structural similarity is not a definitive proxy for energy basins in conformational analysis.
- Principal coordinate analysis is a valuable visualization tool, performing better with dihedral angle distances.
- The reliability of geometric clustering for representing energetic landscapes requires careful consideration.