iCn3D Basics: File Types
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File, Retrieve by ID
MMDB
- MMDB (Molecular Modeling Database) files from the NCBI
- derived from PDB atomic coordinates but with …
- Database information (quaternary struct, molecular interactions, SNPs, conserved domains, clinical variants – i.e related structure info, not just xyz coord
PDB
- xyz coordinates
RCSB MMTF ID (fast)
- Great for very big structures that otherwise too slow in loading; Few modeling options.
AlphaFold Structure
- Computationally determined structures
- Uses Uniprot or RCSB ID.
OPM PDB ID
- Get structures on membrane proteins
Other Membrane Protein Links
•Eukaryotic peripheral membrane proteins (PerMemDB)
•Orientation of proteins in membranes (OPM)
•PDBTM: Protein Data Bank of Transmembrane Proteins
•mpstruct: Membrane Proteins of Known Structure
•Membranome: Membrane proteome of single helix membrane proteins
•MemProtMD: A database of membrane proteins embedded in lipid bilayers
with lipids obtained in Molecular Dynamics simulation