DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism
Abstract 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 ar...
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| Format: | Article |
| Language: | English |
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BMC
2019-06-01
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| Series: | Journal of Cheminformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13321-019-0362-7 |
| _version_ | 1818791815417954304 |
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| author | Eric W. Bell Yang Zhang |
| author_facet | Eric W. Bell Yang Zhang |
| author_sort | Eric W. Bell |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-18T15:17:21Z |
| format | Article |
| id | doaj.art-3dae24d8ad434a40ba6c1ea5c57e05eb |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-18T15:17:21Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-3dae24d8ad434a40ba6c1ea5c57e05eb2022-12-21T21:03:29ZengBMCJournal of Cheminformatics1758-29462019-06-011111910.1186/s13321-019-0362-7DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphismEric W. Bell0Yang Zhang1Department of Computational Medicine and Bioinformatics, University of MichiganDepartment of Computational Medicine and Bioinformatics, University of MichiganAbstract 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.http://link.springer.com/article/10.1186/s13321-019-0362-7Symmetric moleculesProtein–ligand dockingLigand pose comparison |
| spellingShingle | Eric W. Bell Yang Zhang DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism Journal of Cheminformatics Symmetric molecules Protein–ligand docking Ligand pose comparison |
| title | DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism |
| title_full | DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism |
| title_fullStr | DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism |
| title_full_unstemmed | DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism |
| title_short | DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism |
| title_sort | dockrmsd an open source tool for atom mapping and rmsd calculation of symmetric molecules through graph isomorphism |
| topic | Symmetric molecules Protein–ligand docking Ligand pose comparison |
| url | http://link.springer.com/article/10.1186/s13321-019-0362-7 |
| work_keys_str_mv | AT ericwbell dockrmsdanopensourcetoolforatommappingandrmsdcalculationofsymmetricmoleculesthroughgraphisomorphism AT yangzhang dockrmsdanopensourcetoolforatommappingandrmsdcalculationofsymmetricmoleculesthroughgraphisomorphism |