- Structure Comparison
- Structural alignment identifies similarities between protein structures
- Superposition displays structures using criteria from previous alignments
- RMSD calculation measures structural similarity between proteins
- Primary Databases
- NCBI Protein contains protein sequences
- RCSB-PDB is major structural primary database
- Uniprot serves as metadatabase with comprehensive protein information
- Sequence Databases
- Uniprot provides comprehensive protein sequences with annotation
- Pfam classifies proteins by evolutionary relationships using HMM profiles
- InterPro combines multiple databases for protein classification
- Structure Databases
- PDB contains protein structures from various sources
- SCOP organizes protein domains hierarchically
- CATH classifies protein domains using sequence and structure information
- Database Features
- Most databases offer programmatic access and API capabilities
- Most databases contain cross-references to other databases
- Updates occur regularly through snapshots and full releases