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Biology LibreTexts

iCn3D Basics: File Types

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File, Retrieve by ID

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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


iCn3D Basics: File Types is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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