The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.
DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism
Open accessAbstract
Comparison of ligand poses generated by protein-ligand docking programs has often been carried out with the assumption of direct atomic correspondence between ligand structures. However, this correspondence is not necessarily chemically relevant for symmetric molecules and can lead to an artificial inflation of ligand pose distance metrics, particularly those that depend on receptor superposition (rather than ligand superposition), such as docking root mean square deviation (RMSD). Several of the commonly-used RMSD calculation algorithms that correct for molecular symmetry do not take into account the bonding structure of molecules and can therefore result in non-physical atomic mapping. Here, we present DockRMSD, a docking pose distance calculator that converts the symmetry correction to a graph isomorphism searching problem, in which the optimal atomic mapping and RMSD calculation are performed by an exhaustive and fast matching search of all isomorphisms of the ligand structure graph. We show through evaluation of docking poses generated by AutoDock Vina on the CSAR Hi-Q set that DockRMSD is capable of deterministically identifying the minimum symmetry-corrected RMSD and is able to do so without significant loss of computational efficiency compared to other methods. The open-source DockRMSD program can be conveniently integrated with various docking pipelines to assist with accurate atomic mapping and RMSD calculations, which can therefore help improve docking performance, especially for ligand molecules with complicated structural symmetry.
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
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,828
Trott, O., & Olson, A. J. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21334 · Cited by 38,412
The Hungarian method for the assignment problem
Kuhn, H. W. (1955) · Naval Research Logistics Quarterly · doi:10.1002/nav.3800020109 · Cited by 13,120
Open Babel: An open chemical toolbox
O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011) · Journal of Cheminformatics · doi:10.1186/1758-2946-3-33 · Cited by 10,939
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
Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm030644s · Cited by 5,177
Algorithms for the Assignment and Transportation Problems
Munkres, J. (1957) · Journal of the Society for Industrial and Applied Mathematics · doi:10.1137/0105003 · Cited by 3,986
A (sub)graph isomorphism algorithm for matching large graphs
Cordella, L. P., Foggia, P., Sansone, C., & Vento, M. (2004) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2004.75 · Cited by 1,477
DOCK 6: Impact of new features and current docking performance
Allen, W. J., Balius, T. E., Mukherjee, S., Brozell, S. R., Moustakas, D. T., Lang, P. T., Case, D. A., Kuntz, I. D., & Rizzo, R. C. (2015) · Journal of Computational Chemistry · doi:10.1002/jcc.23905 · Cited by 833
Cited by
FitDock: protein–ligand docking by template fitting
Yang, X., Liu, Y., Gan, J., Xiao, Z.-X., & Cao, Y. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac087 · Cited by 319
Structure prediction of protein-ligand complexes from sequence information with Umol
Bryant, P., Kelkar, A., Guljas, A., Clementi, C., & Noé, F. (2024) · Nature Communications · doi:10.1038/s41467-024-48837-6 · Cited by 75
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts
Karimi, M., Wu, D., Wang, Z., & Shen, Y. (2019) · doi:10.1101/2019.12.28.890103 · Cited by 64
Explainable Deep Relational Networks for Predicting Compound–Protein Affinities and Contacts
Karimi, M., Wu, D., Wang, Z., & Shen, Y. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00866 · Cited by 64
Assessing the binding properties of CASP14 targets and models
Egbert, M., Ghani, U., Ashizawa, R., Kotelnikov, S., Nguyen, T., Desta, I., Hashemi, N., Padhorny, D., Kozakov, D., & Vajda, S. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26209 · Cited by 10
Metadata
- Authors
- Bell, E. W., & Zhang, Y.
- Venue
- Journal of Cheminformatics
- Published
- 2019-06-07
- Volume
- 11
- Issue
- 1
- Pages
- 40-40
- ISSN
- 1758-2946 (ISSN-L)
- OpenAlex
- W2954297401
- Cited by
- 462
- References
- 19
- FWCI
- 18.99
- Type
- journal article
- Language
- en
- Open access
- gold
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: DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. https://app.cochat.ai/papers/10.1186/s13321-019-0362-7
- The paper
- Bell, E. W., & Zhang, Y. (2019). DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. Journal of Cheminformatics. https://doi.org/10.1186/s13321-019-0362-7
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.
