The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Physics-Based Scoring of Protein−Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening
Abstract
We demonstrate that using an all-atom molecular mechanics force field combined with an implicit solvent model for scoring protein-ligand complexes is a promising approach for improving inhibitor enrichment in the virtual screening of large compound databases. The rescoring method is evaluated by the extent to which known binders for nine diverse, therapeutically relevant enzymes are enriched against a background of approximately 100,000 drug-like decoys. The improvement in enrichment is most robust and dramatic within the top 1% of the ranked database, that is, the first thousand compounds; below the first few percent of the ranked database, there is little overall improvement. The improved early enrichment is likely due to the more realistic treatment of ligand and receptor desolvation in the rescoring procedure. We also present anecdotal but encouraging results assessing the ability of the rescoring method to predict specificity of inhibitors for structurally related proteins.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., et al. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0306430 · Cited by 10,057
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0897 · Cited by 6,763
Bissantz, C., Folkers, G., & Rognan, D. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm001044l · Cited by 740
Charifson, P. S., Corkery, J. J., Murcko, M. A., & Walters, W. P. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm990352k · Cited by 698
Cited by
Huang, S.-Y., Grinter, S. Z., & Zou, X. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp00151a · Cited by 508
Docking Challenge: Protein Sampling and Molecular Docking Performance
Elokely, K. M., & Doerksen, R. J. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400040d · Cited by 287
Lin, X., Huang, X.-P., Chen, G., Whaley, R., Peng, S., Wang, Y., Zhang, G., Wang, S. X., Wang, S., Roth, B. L., et al. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm300338m · Cited by 73
Self-citationScoring Functions for Protein–Ligand Interactions
Sotriffer, C. (2012) · Protein‐Ligand Interactions · doi:10.1002/9783527645947.ch12 · Cited by 16
Metadata
- Authors
- Huang, N., Kalyanaraman, C., Irwin, J. J., & Jacobson, M. P.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2005-11-11
- Volume
- 46
- Issue
- 1
- Pages
- 243-253
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2094162409
- Cited by
- 169
- References
- 4
- FWCI
- 7.22
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
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).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
