Abstract
The absolute free energy-or partition function, equivalently-of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule based on a series of fragments. Significant computer time is saved by precalculating fragment configurations and interactions for reuse in a variety of molecules. We use such fragment libraries and interaction tables for amino acids and capping groups to estimate free energies for small peptides. Equilibrium ensembles for the molecules are generated at no additional computational cost and are used to check our results by comparison to standard dynamics simulation. We explain how our work can be extended to estimate relative binding affinities.
Original language | English (US) |
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Pages (from-to) | 1680-1691 |
Number of pages | 12 |
Journal | Journal of Computational Chemistry |
Volume | 30 |
Issue number | 11 |
DOIs | |
State | Published - Aug 2009 |
Externally published | Yes |
Keywords
- Absolute free energy
- Alanine dipeptide
- Molecular fragment libraries
- Polymer growth
- Tetra-alanine
ASJC Scopus subject areas
- General Chemistry
- Computational Mathematics