Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules
Abstract Small-molecule protonation can promote or discourage protein binding by altering hydrogen-bond, electrostatic, and van-der-Waals interactions. To improve virtual-screen pose and affinity predictions, researchers must account for all major small-molecule ionization states. But existing progr...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-02-01
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| Series: | Journal of Cheminformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13321-019-0336-9 |
| _version_ | 1819289558767894528 |
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| author | Patrick J. Ropp Jesse C. Kaminsky Sara Yablonski Jacob D. Durrant |
| author_facet | Patrick J. Ropp Jesse C. Kaminsky Sara Yablonski Jacob D. Durrant |
| author_sort | Patrick J. Ropp |
| collection | DOAJ |
| description | Abstract Small-molecule protonation can promote or discourage protein binding by altering hydrogen-bond, electrostatic, and van-der-Waals interactions. To improve virtual-screen pose and affinity predictions, researchers must account for all major small-molecule ionization states. But existing programs for calculating these states have notable limitations such as high cost, restrictive licenses, slow execution times, and poor modularity. Here, we present dimorphite-DL 1.0, a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states. Dimorphite-DL uses a straightforward empirical algorithm that leverages substructure searching and draws on a database of experimentally characterized ionizable molecules. We have tested dimorphite-DL using several versions of Python and RDKit on all major operating systems. We release it under the terms of the Apache License, Version 2.0. A copy is available free of charge from http://durrantlab.com/dimorphite-dl/. |
| first_indexed | 2024-12-24T03:08:46Z |
| format | Article |
| id | doaj.art-6f877da85ae14b6394a14f5332335fc4 |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-24T03:08:46Z |
| publishDate | 2019-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-6f877da85ae14b6394a14f5332335fc42022-12-21T17:17:54ZengBMCJournal of Cheminformatics1758-29462019-02-011111810.1186/s13321-019-0336-9Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small moleculesPatrick J. Ropp0Jesse C. Kaminsky1Sara Yablonski2Jacob D. Durrant3Department of Biological Sciences, University of PittsburghDepartment of Biological Sciences, University of PittsburghDepartment of Biological Sciences, University of PittsburghDepartment of Biological Sciences, University of PittsburghAbstract Small-molecule protonation can promote or discourage protein binding by altering hydrogen-bond, electrostatic, and van-der-Waals interactions. To improve virtual-screen pose and affinity predictions, researchers must account for all major small-molecule ionization states. But existing programs for calculating these states have notable limitations such as high cost, restrictive licenses, slow execution times, and poor modularity. Here, we present dimorphite-DL 1.0, a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states. Dimorphite-DL uses a straightforward empirical algorithm that leverages substructure searching and draws on a database of experimentally characterized ionizable molecules. We have tested dimorphite-DL using several versions of Python and RDKit on all major operating systems. We release it under the terms of the Apache License, Version 2.0. A copy is available free of charge from http://durrantlab.com/dimorphite-dl/.http://link.springer.com/article/10.1186/s13321-019-0336-9IonizationpHProtonationModelingVirtual screeningDrug discovery |
| spellingShingle | Patrick J. Ropp Jesse C. Kaminsky Sara Yablonski Jacob D. Durrant Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules Journal of Cheminformatics Ionization pH Protonation Modeling Virtual screening Drug discovery |
| title | Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules |
| title_full | Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules |
| title_fullStr | Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules |
| title_full_unstemmed | Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules |
| title_short | Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules |
| title_sort | dimorphite dl an open source program for enumerating the ionization states of drug like small molecules |
| topic | Ionization pH Protonation Modeling Virtual screening Drug discovery |
| url | http://link.springer.com/article/10.1186/s13321-019-0336-9 |
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