ArticleProceedings of the National Academy of Sciences of the United States of America2008
A black-box re-weighting analysis can correct flawed simulation data.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- ModBindProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Equilibrium molecular thermodynamics from Kirkwood sampling.The journal of physical chemistry. B · 2015Article
- Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.Nature chemistry · 2014Article
- Population based reweighting of scaled molecular dynamics.The journal of physical chemistry. B · 2013Article
- Understanding the structural ensembles of a highly extended disordered protein.Molecular bioSystems · 2012Article
- Equilibrium sampling in biomolecular simulations.Annual review of biophysics · 2011Review
- Rapid equilibrium sampling initiated from nonequilibrium data.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
There is a great need for improved statistical sampling in a range of physical, chemical, and biological systems. Even simulations based on correct algorithms suffer from statistical error, which can be substantial or even dominant when slow processes are involved. Further, in key biomolecular applications, such as the determination of protein structures from NMR data, non-Boltzmann-distributed ensembles are generated. We therefore have developed the "black-box" strategy for re-weighting a set of configurations generated by arbitrary means to produce an ensemble distributed according to any target distribution. In contrast to previous algorithmic efforts, the black-box approach exploits the configuration-space density observed in a simulation, rather than assuming a desired distribution has been generated. Successful implementations of the strategy, which reduce both statistical error and bias, are developed for a one-dimensional system, and a 50-atom peptide, for which the correct 250-to-1 population ratio is recovered from a heavily biased ensemble.
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Registered trials
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