The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
Open accessAbstract
In the past few decades, many ingenious efforts have been made in the development of free-energy simulation methods. Because complex systems often undergo nontrivial structural transition during state switching, achieving efficient free-energy calculation can be challenging. As identified earlier, the “Hamiltonian” lagging, which reveals the fact that necessary structural relaxation falls behind the order parameter move, has been a primary problem for generally low free-energy simulation efficiency. Here, we propose an algorithm by achieving a random walk in both the order parameter space and its generalized force space; thereby, the order parameter move and the required conformational relaxation can be efficiently synchronized. As demonstrated in both the alchemical transition and the conformational transition, a leapfrog improvement in free-energy simulation efficiency can be obtained; for instance, ( i ) it allows us to solve a notoriously challenging problem: accurately predicting the pK a value of a buried titratable residue, Asp-66, in the interior of the V66E staphylococcal nuclease mutant, and ( ii ) it allows us to gain superior efficiency over the metadynamics algorithm.
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Cites
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Cited by
Wang, L., Wu, Y., Deng, Y., Kim, B., Pierce, L., Krilov, G., Lupyan, D., Robinson, S., Dahlgren, M. K., Greenwood, J., et al. (2015) · Journal of the American Chemical Society · doi:10.1021/ja512751q · Cited by 1,313
Using collective variables to drive molecular dynamics simulations
Fiorin, G., Klein, M. L., & Hénin, J. (2013) · Molecular Physics · doi:10.1080/00268976.2013.813594 · Cited by 1,053
Brunk, E., & Rothlisberger, U. (2015) · Chemical Reviews · doi:10.1021/cr500628b · Cited by 494
Large shifts in pK a values of lysine residues buried inside a protein
Isom, D. G., Castañeda, C. A., Cannon, B. R., & García-Moreno E., B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1010750108 · Cited by 466
In silico ADME/T modelling for rational drug design
Wang, Y., Xing, J., Xu, Y., Zhou, N., Peng, J., Xiong, Z., Liu, X., Luo, X., Luo, C., Chen, K., et al. (2015) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583515000190 · Cited by 367
Metadata
- Authors
- Zheng, L., Chen, M., & Yang, W.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2008-12-23
- Volume
- 105
- Issue
- 51
- Pages
- 20227-20232
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1984604072
- Cited by
- 310
- References
- 18
- FWCI
- 6.58
- Type
- journal article
- Language
- en
- Open access
- green
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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