ArticleJournal of computational chemistry2009
Absolute free energies estimated by combining precalculated molecular fragment libraries.
Article in Journal of computational chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Systematic Testing of Belief-Propagation Estimates for Absolute Free Energies in Atomistic Peptides and Proteins.Journal of chemical theory and computation · 2018Article
- Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.The Journal of chemical physics · 2014Article
- Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.Journal of chemical theory and computation · 2012Article
- Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.Journal of computational chemistry · 2011Article
- Accelerated convergence of molecular free energy via superposition approximation-based reference states.The Journal of chemical physics · 2011Article
- Rapid sampling of all-atom peptides using a library-based polymer-growth approach.Journal of computational chemistry · 2011Article
- Automated sampling assessment for molecular simulations using the effective sample size.Journal of chemical theory and computation · 2010Article
- Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo.The journal of physical chemistry. B · 2010Article
- Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method.The Journal of chemical physics · 2009Article
- General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models.The journal of physical chemistry. B · 2009Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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.
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Registered trials
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