Databases

Covalent

• CovPDB: covalent protein-ligand interactome

  

Data Mining

• Lemon: a framework for rapidly mining structural information from the Protein Data Bank (standalone)
  

  

• PDBminer: PDBminer to Find and Annotate Protein Structures for Computational Analysis
  

  

Databases

• EMDB: Electron Microscopy Data Bank

  

  

• PDB: The RCSB Protein Data Bank provides access to experimentally determined 3D structures from the PDB archive and computed structure models, offering tools for exploration, visualization, and analysis.

  

  

• PDB-redo: Offers optimized versions of PDB entries through an automated procedure that refines, rebuilds, and validates structural models, combining popular crystallographic software with specially developed tools.

  

  

• PDBe: PDBe: improved findability of macromolecular structure data in the PDB

  

  

Viruses

• Viro3D: