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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Geometry optimization for peptides and proteins: comparison of Cartesian and internal coordinates
Elena F Koslover1, David J Wales
1University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
The Journal of Chemical Physics
|December 25, 2007
Summary
Coordinate systems impact polypeptide geometry optimization efficiency. Internal coordinates excel for small peptides, while Cartesian coordinates are more efficient for larger biomolecules using empirical potentials.
Area of Science:
- Computational chemistry
- Biomolecular modeling
- Structural biology
Background:
- Optimizing polypeptide geometries is crucial for understanding biomolecular structure and function.
- Different coordinate systems (Cartesian, internal) offer distinct advantages and disadvantages for molecular mechanics calculations.
- The choice of coordinate system can significantly influence computational efficiency.
Purpose of the Study:
- To benchmark the relative efficiency of Cartesian, natural internal, and primitive internal coordinate systems for polypeptide geometry optimization.
- To evaluate how system size and complexity affect the performance of different coordinate systems.
- To determine the optimal coordinate system strategy for various biomolecular modeling scenarios.
Main Methods:
- Quasi-Newton minimization algorithm applied to diverse biomolecules.
- Systematic comparison of computational performance across different coordinate systems.
- Benchmarking conducted on peptides and proteins ranging from 16 to 999 residues.
Main Results:
- The efficiency of coordinate systems is dependent on optimization parameters, starting points, and system size.
- Internal coordinates demonstrated advantages for optimizing smaller peptide structures.
- Cartesian coordinates proved more efficient for larger biomolecules, especially with fast energy/gradient evaluations.
Conclusions:
- No single coordinate system is universally superior for all polypeptide geometry optimizations.
- The optimal choice involves balancing coordinate system properties with computational cost and system characteristics.
- Internal coordinates are recommended for small peptides, while Cartesian coordinates are favored for large proteins with empirical potentials.
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