Cross-species molecular docking method to support predictions of species susceptibility to chemical effects
The advancement of protein structural prediction tools, exemplified by AlphaFold and Iterative Threading ASSEmbly Refinement, has enabled the prediction of protein structures across species based on available protein sequence and structural data. In this study, we introduce an innovative molecular docking method that capitalizes on this wealth of structural data to enhance predictions of chemical susceptibility across species. We demonstrated this method using the androgen receptor as a pertinent modulator of endocrine function. By using protein structures, this method contextualizes species susceptibility within a functional framework and helps to integrate molecular docking into the repertoire of New Approach Methodologies (NAMs) that support the Next-Generation Risk Assessment (NGRA) paradigm through the novel integration of various open-source tools.
This dataset is associated with the following publication:
Schumann, P., D. Chang, S. Mayasich, S. Vliet, T. Brown, and C. LaLone. Cross-species molecular docking method to support predictions of species susceptibility to chemical effects. Computational Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 30(4): 100319, (2024).
Resources
4 resources available
-
https://github.com/pschumann4/cross_species_docking.git
FILE -
1-s2.0-S2468111324000215-mmc1.docx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.WORDPROCESSINGML.DOCUMENT -
1-s2.0-S2468111324000215-mmc2.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET -
1-s2.0-S2468111324000215-mmc3.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "020:00" ] |
| contactPoint |
{ "fn": "Carlie LaLone", "hasEmail": "mailto:lalone.carlie@epa.gov" } |
| description | The advancement of protein structural prediction tools, exemplified by AlphaFold and Iterative Threading ASSEmbly Refinement, has enabled the prediction of protein structures across species based on available protein sequence and structural data. In this study, we introduce an innovative molecular docking method that capitalizes on this wealth of structural data to enhance predictions of chemical susceptibility across species. We demonstrated this method using the androgen receptor as a pertinent modulator of endocrine function. By using protein structures, this method contextualizes species susceptibility within a functional framework and helps to integrate molecular docking into the repertoire of New Approach Methodologies (NAMs) that support the Next-Generation Risk Assessment (NGRA) paradigm through the novel integration of various open-source tools. This dataset is associated with the following publication: Schumann, P., D. Chang, S. Mayasich, S. Vliet, T. Brown, and C. LaLone. Cross-species molecular docking method to support predictions of species susceptibility to chemical effects. Computational Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 30(4): 100319, (2024). |
| distribution |
[ { "title": "https://github.com/pschumann4/cross_species_docking.git", "accessURL": "https://github.com/pschumann4/cross_species_docking.git" }, { "title": "1-s2.0-S2468111324000215-mmc1.docx", "mediaType": "application/vnd.openxmlformats-officedocument.wordprocessingml.document", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1531089/1-s2.0-S2468111324000215-mmc1.docx" }, { "title": "1-s2.0-S2468111324000215-mmc2.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1531089/1-s2.0-S2468111324000215-mmc2.xlsx" }, { "title": "1-s2.0-S2468111324000215-mmc3.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1531089/1-s2.0-S2468111324000215-mmc3.xlsx" } ] |
| identifier | https://doi.org/10.23719/1531089 |
| keyword |
[ "Androgen receptor", "Molecular Docking", "New Approach Methods", "Next Generation Risk Assessment", "SeqAPASS", "Species Extrapolation", "bioinformatics", "case studies", "endocrine", "molecular modelling", "regulation" ] |
| license | https://pasteur.epa.gov/license/sciencehub-license.html |
| modified | 2024-05-26 |
| programCode |
[ "020:000" ] |
| publisher |
{ "name": "U.S. EPA Office of Research and Development (ORD)", "subOrganizationOf": { "name": "U.S. Environmental Protection Agency", "subOrganizationOf": { "name": "U.S. Government" } } } |
| references |
[ "https://doi.org/10.1016/j.comtox.2024.100319" ] |
| rights |
null
|
| title | Cross-species molecular docking method to support predictions of species susceptibility to chemical effects |
