pdb-database
PDB Database
Overview
RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules. Search for structures, retrieve coordinates and metadata, perform sequence and structure similarity searches across 200,000+ experimentally determined structures and computed models.
When to Use This Skill
This skill should be used when:
- Searching for protein or nucleic acid 3D structures by text, sequence, or structural similarity
- Downloading coordinate files in PDB, mmCIF, or BinaryCIF formats
- Retrieving structural metadata, experimental methods, or quality metrics
- Performing batch operations across multiple structures
- Integrating PDB data into computational workflows for drug discovery, protein engineering, or structural biology research
Core Capabilities
1. Searching for Structures
More from jimmc414/kosmos
scientific-schematics
Create publication-quality scientific diagrams, flowcharts, and schematics using Python (graphviz, matplotlib, schemdraw, networkx). Specialized in neural network architectures, system diagrams, and flowcharts. Generates SVG/EPS in figures/ folder with automated quality verification.
32pptx
Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
18ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
17docx
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
15scientific-slides
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
13scientific-visualization
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
12