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rPDBapi", "author": "Selcuk Korkmaz, Bilge Eren Yamasan", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation and Setup", "Why Access the PDB from R?", "rPDBapi Capabilities", "Package Feature Map", "Core Concepts in the RCSB PDB API", "Workflow 1: Simple Search for Kinase Structures", "Workflow 2: Refine the Search with Structured Operators", "Workflow 3: Retrieve Entry-Level Metadata", "Workflow 4: Inspect the Raw API Payload and Convert It to Tidy Data", "Workflow 4b: Batch Retrieval, Provenance, and Cache-Aware Access", "Workflow 5: Retrieve Assembly-Level Data", "Workflow 5b: Identifier-Aware Retrieval Patterns", "Workflow 6: Retrieve Taxonomy and Chain-Level Biological Context", "Workflow 7: Retrieve Detailed Entry Annotations", "Workflow 8: Download Coordinates and Inspect Atomic Data", "Workflow 8b: Working with the Rich Object Model", "Workflow 9: Downstream Analysis in R", "Workflow 10: Optional Visualization with r3dmol", "Advanced Search Modalities", 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