ArticleThe journal of physical chemistry. B2017
Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 13 citations in OpenAlex.
- Water Networks in Complexes between Proteins and FDA-Approved Drugs.Journal of chemical information and modeling · 2023Article
- The catalytic mechanism of the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2).PLoS computational biology · 2022Article
- Exploring the Effectiveness of Binding Free Energy Calculations.The journal of physical chemistry. B · 2019Article
- Revisiting the protomotive vectorial motion of FProceedings of the National Academy of Sciences of the United States of America · 2019Article
- On the control of the proton current in the voltage-gated proton channel Hv1.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- EF-Tu and EF-G are activated by allosteric effects.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The study of the function of proteins on a quantitative level requires consideration of the water molecules in and around the protein. This requirement presents a major computational challenge due to the fact that the insertion of water molecules can have a very high activation barrier and would require a long simulation time. Recently, we developed a water flooding (WF) approach which is based on a postprocessing Monte Carlo ranking of possible water configurations. This approach appears to provide a very effective way for assessing the insertion free energies and determining the most likely configurations of the internal water molecules. Although the WF approach was used effectively in modeling challenging systems that have not been addressed reliably by other microscopic approaches, it was not validated by a comparison to the more rigorous grand canonical Monte Carlo (GCMC) method. Here we validate the WF approach by comparing its performance to that of the GCMC method. It is found that the WF approach reproduces the GCMC results in well-defined test cases but does so much faster. This established the WF approach as a useful strategy for finding correct water configurations in proteins and thus to provide a powerful way for studies of the functions of proteins.
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