Making protein dynamics FAIR : Research platforms for the collection, dissemination, and analysis of molecular dynamics simulations
Molecular dynamics (MD) simulations are a well-established technique to characterize the structural motions of biological systems at atomic resolution. However, accessing, viewing, and sharing MD trajectories is typically restricted by large file sizes and the need for specialized software, which li...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2022 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/673525 |
| Acceso en línea: | http://hdl.handle.net/10803/673525 |
| Access Level: | acceso abierto |
| Palabra clave: | Molecular dynamics simulations Simulacions de dinàmica molecular Online repository Repositori online G protein-coupled receptors Receptors acoblats a proteïnes G SARS-CoV-2 Data sharing Compartició de dades 577 |
| Sumario: | Molecular dynamics (MD) simulations are a well-established technique to characterize the structural motions of biological systems at atomic resolution. However, accessing, viewing, and sharing MD trajectories is typically restricted by large file sizes and the need for specialized software, which limits the audience to which this data is available. The aim of this thesis is to extend the outreach of MD simulations by providing online resources that facilitate the dissemination, visual inspection, and analysis of this data. For that, we present GPCRmd and SCoV2-MD, two online resources focused on proteins with high biomedical interest: G protein-coupled receptors (GPCRs) and the proteome of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), respectively. We also showcase the capabilities of GPCRmd and SCoV2-MD for exploring key aspects of protein dynamics. Overall, these platforms have the potential to promote data “Findability, Accessibility, Interoperability, and Reusability” in the MD field, supporting the FAIR principles for scientific data management. |
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