Input files, parameters, and scripts used for the computational mapping and targeting of BK channel protein–protein interactions in breast cancer
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2026
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| _version_ | 1866901695116607488 |
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| author | Vergara-Jaque, Ariela González-Avendaño, Mariela Rosales-Rojas, Roberto |
| author_facet | Vergara-Jaque, Ariela González-Avendaño, Mariela Rosales-Rojas, Roberto |
| contents | <p><strong>1. Identification of differentially expressed genes in breast cancer cells: </strong>R scripts and output files used to identify differentially expressed genes from the GSE71862 RNA-seq dataset using DESeq2.</p> <p><strong>2. Construction of protein interaction networks to identify BK channel partners: </strong>Files used to build and analyze BK-centered protein–protein interaction networks and to prioritize candidate interactors based on functional and disease relevance.</p> <p><strong>3. Identification of protein-protein contact regions: </strong>Scripts and outputs used to identify consensus interface residues between the BK channel and selected partners from multiple computational predictors.</p> <p><strong>4. Molecular docking of protein-protein interactions: </strong>Input structures, docking configurations, and representative models generated for BK complexes using HADDOCK and Rosetta MPDock.</p> <p><strong>5. Coarse-grained molecular dynamics simulations: </strong>System setup files and simulation inputs used for coarse-grained molecular dynamics simulations of BK protein complexes in a lipid bilayer.</p> <p><strong>6. Design of peptide inhibitors of the BK-LINGO1 complex: </strong>Input/output files used for de novo peptide design targeting the BK–LINGO1 interface and for subsequent binding evaluation by molecular dynamics and MM/GBSA.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18315809 |
| institution | Zenodo |
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| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Input files, parameters, and scripts used for the computational mapping and targeting of BK channel protein–protein interactions in breast cancer Vergara-Jaque, Ariela González-Avendaño, Mariela Rosales-Rojas, Roberto <p><strong>1. Identification of differentially expressed genes in breast cancer cells: </strong>R scripts and output files used to identify differentially expressed genes from the GSE71862 RNA-seq dataset using DESeq2.</p> <p><strong>2. Construction of protein interaction networks to identify BK channel partners: </strong>Files used to build and analyze BK-centered protein–protein interaction networks and to prioritize candidate interactors based on functional and disease relevance.</p> <p><strong>3. Identification of protein-protein contact regions: </strong>Scripts and outputs used to identify consensus interface residues between the BK channel and selected partners from multiple computational predictors.</p> <p><strong>4. Molecular docking of protein-protein interactions: </strong>Input structures, docking configurations, and representative models generated for BK complexes using HADDOCK and Rosetta MPDock.</p> <p><strong>5. Coarse-grained molecular dynamics simulations: </strong>System setup files and simulation inputs used for coarse-grained molecular dynamics simulations of BK protein complexes in a lipid bilayer.</p> <p><strong>6. Design of peptide inhibitors of the BK-LINGO1 complex: </strong>Input/output files used for de novo peptide design targeting the BK–LINGO1 interface and for subsequent binding evaluation by molecular dynamics and MM/GBSA.</p> |
| title | Input files, parameters, and scripts used for the computational mapping and targeting of BK channel protein–protein interactions in breast cancer |
| url | https://doi.org/10.5281/zenodo.18315809 |