The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.
Flexible Docking in Solution Using Metadynamics
Abstract
We apply our recently developed metadynamics method to the docking of ligands on flexible receptors in water solution. This method mimics the real dynamics of a ligand exiting or entering an enzyme and in so doing reconstructs the free energy surface. We apply it to four docking cases: beta-trypsin/benzamidine, beta-trypsin/chlorobenzamidine, immunoglobulin McPC-603/phosphocholine, and cyclin-dependent kinase 2/staurosporine. In every case studied, the method is able to predict the docked geometry and the free energy of docking. Its added value with respect to many other available methods is that it reconstructs the complete free energy surface, including all the relevant minima and the barriers between them.
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Cites
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Self-citationA Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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Cited by
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
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Self-citationEnhanced sampling techniques in molecular dynamics simulations of biological systems
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Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Buch, I., Giorgino, T., & De Fabritiis, G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1103547108 · Cited by 655
Molecular dynamics simulations and novel drug discovery
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Metadata
- Authors
- Gervasio, F. L., Laio, A., & Parrinello, M.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2005-02-05
- Volume
- 127
- Issue
- 8
- Pages
- 2600-2607
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2069982778
- Cited by
- 287
- References
- 44
- FWCI
- 13.49
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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