The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
How to do an evaluation: pitfalls and traps
Open accessAbstract
The recent literature is replete with papers evaluating computational tools (often those operating on 3D structures) for their performance in a certain set of tasks. Most commonly these papers compare a number of docking tools for their performance in cognate re-docking (pose prediction) and/or virtual screening. Related papers have been published on ligand-based tools: pose prediction by conformer generators and virtual screening using a variety of ligand-based approaches. The reliability of these comparisons is critically affected by a number of factors usually ignored by the authors, including bias in the datasets used in virtual screening, the metrics used to assess performance in virtual screening and pose prediction and errors in crystal structures used.
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
Benchmarking sets for molecular docking.
Huang, N., Shoichet, B. K., & Irwin, J. J. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm0608356 · Cited by 1,318
Bissantz, C., Folkers, G., & Rognan, D. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm001044l · Cited by 740
Cited by
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.
Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm300687e · Cited by 2,412
Recognizing Pitfalls in Virtual Screening: A Critical Review
Scior, T., Bender, A., Tresadern, G., Medina-Franco, J. L., Martínez-Mayorga, K., Langer, T., Cuanalo-Contreras, K., & Agrafiotis, D. K. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci200528d · Cited by 438
Damm-Ganamet, K. L., Smith, R. D., Dunbar, J. B., Stuckey, J. A., & Carlson, H. A. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400025f · Cited by 133
Zheng, H., Shabalin, I. G., Handing, K. B., Bujnicki, J. M., & Minor, W. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv225 · Cited by 107
Lagarde, N., Zagury, J.-F., & Montes, M. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00090 · Cited by 85
Metadata
- Authors
- Hawkins, P. C. D., Warren, G. L., Skillman, A. G., & Nicholls, A.
- Venue
- Journal of Computer-Aided Molecular Design
- Published
- 2008-01-23
- Volume
- 22
- Issue
- 3-4
- Pages
- 179-190
- ISSN
- 0920-654X (ISSN-L)
- 1573-4951
- OpenAlex
- W2058433776
- Cited by
- 166
- References
- 4
- FWCI
- 25.26
- Type
- journal article
- Language
- en
- Open access
- hybrid
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: How to do an evaluation: pitfalls and traps. https://app.cochat.ai/papers/10.1007/s10822-007-9166-3
- The paper
- Hawkins, P. C. D., Warren, G. L., Skillman, A. G., & Nicholls, A. (2008). How to do an evaluation: pitfalls and traps. Journal of Computer-Aided Molecular Design. https://doi.org/10.1007/s10822-007-9166-3
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.
