The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
Abstract
We present a novel protein-ligand docking method that accurately accounts for both ligand and receptor flexibility by iteratively combining rigid receptor docking (Glide) with protein structure prediction (Prime) techniques. While traditional rigid-receptor docking methods are useful when the receptor structure does not change substantially upon ligand binding, success is limited when the protein must be "induced" into the correct binding conformation for a given ligand. We provide an in-depth description of our novel methodology and present results for 21 pharmaceutically relevant examples. Traditional rigid-receptor docking for these 21 cases yields an average RMSD of 5.5 A. The average ligand RMSD for docking to a flexible receptor for the 21 pairs is 1.4 A; the RMSD is < or =1.8 A for 18 of the cases. For the three cases with RMSDs greater than 1.8 A, the core of the ligand is properly docked and all key protein/ligand interactions are captured.
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
Self-citationImplications of protein flexibility for drug discovery
Teague, S. J. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1129 · Cited by 755
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
Kellenberger, E., Rodrigo, J., Muller, P., & Rognan, D. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20149 · Cited by 577
Cited by
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011) · Current Computer Aided-Drug Design · doi:10.2174/157340911795677602 · Cited by 3,771
Improved Docking of Polypeptides with Glide
Tubert-Brohman, I., Sherman, W., Repasky, M., & Beuming, T. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400128m · Cited by 1,308
Self-citationClass I histone deacetylases (HDAC1–3) are histone lysine delactylases
Moreno-Yruela, C., Zhang, D., Wei, W., Bæk, M., Liu, W., Gao, J., Danková, D., Nielsen, A. L., Bolding, J. E., Yang, L., et al. (2022) · Science Advances · doi:10.1126/sciadv.abi6696 · Cited by 841
Moitessier, N., Englebienne, P., Lee, D., Lawandi, J., & Corbeil, C. R. (2008) · British Journal of Pharmacology · doi:10.1038/sj.bjp.0707515 · Cited by 514
Flexible ligand docking to multiple receptor conformations: a practical alternative
Totrov, M., & Abagyan, R. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.01.004 · Cited by 497
Metadata
- Authors
- Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., & Farid, R.
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2005-12-23
- Volume
- 49
- Issue
- 2
- Pages
- 534-553
- ISSN
- 0022-2623 (ISSN-L)
- 1520-4804
- OpenAlex
- W1975691556
- Cited by
- 2,031
- References
- 3
- FWCI
- 34.52
- 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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects. https://app.cochat.ai/papers/10.1021/jm050540c
- The paper
- Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., & Farid, R. (2006). Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects. Journal of Medicinal Chemistry. https://doi.org/10.1021/jm050540c
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.
