The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
Open accessAbstract
We review insights from computational studies of affinities of ligands binding to proteins. The power of structural biology is in translating knowledge of protein structures into insights about their forces, binding, and mechanisms. However, the complementary power of computer modeling is in showing “the rest of the story” (i.e., how motions and ensembles and alternative conformers and the entropies and forces that cannot be seen in single molecular structures also contribute to binding affinities). Upon binding to a protein, a ligand can bind in multiple orientations; the protein or ligand can be deformed by the binding event; waters, ions, or cofactors can have unexpected involvement; and conformational or solvation entropies can sometimes play large and otherwise unpredictable roles. Computer modeling is helping to elucidate these factors.
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Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
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Self-citationPredicting Absolute Ligand Binding Free Energies to a Simple Model Site
Mobley, D. L., Graves, A. P., Chodera, J. D., McReynolds, A. C., Shoichet, B. K., & Dill, K. A. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.06.002 · Cited by 310
Self-citation
Cited by
Molecular Dynamics Simulation for All
Hollingsworth, S. A., & Dror, R. O. (2018) · Neuron · doi:10.1016/j.neuron.2018.08.011 · Cited by 3,257
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Tzeng, S.-R., & Kalodimos, C. G. (2012) · Nature · doi:10.1038/nature11271 · Cited by 545
A practical guide to large-scale docking
Bender, B. J., Gahbauer, S., Luttens, A., Lyu, J., Webb, C. M., Stein, R. M., Fink, E. A., Balius, T. E., Carlsson, J., Irwin, J. J., et al. (2021) · Nature Protocols · doi:10.1038/s41596-021-00597-z · Cited by 546
Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations
Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., & Biggin, P. C. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.6b11467 · Cited by 177
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Metadata
- Authors
- Mobley, D. L., & Dill, K. A.
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2009-04
- Volume
- 17
- Issue
- 4
- Pages
- 489-498
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W2084550263
- Cited by
- 584
- References
- 10
- FWCI
- 14.04
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Mobley, D. L., & Dill, K. A. (2009). Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”. Structure. https://doi.org/10.1016/j.str.2009.02.010
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
