Macromolecular structure databases
Structure databasesDescriptionWeblink
wwPDBWorldwide macromolecular
RCSB PDBMacromolecular
PDBeMacromolecular structures in
PDBjMacromolecular structures in
BMRBMacromolecular structures from
NDBNucleic acid structure
MMDB3D macromolecular
JenaLib3D biopolymer
PDBbind3D macromolecular structures in complex with
IUPHAR/BPS Guide to PHARMACOLOGYPharmacological targets and
ModBaseTheoretical 3D macromolecular
PMPTheoretical 3D macromolecular
SWISS-MODELTheoretical 3D macromolecular
Small molecule databases
Ligand databasesDescriptionWeblink
ZINCOver 35 million purchasable compounds for virtual
PubChemOver 90 million
DrugBankMore than 11,000 drug
SpecsProviding high throughput screening
ChemBridgeOver 1.1 million druglike and leadlike
ChemDivOver 1,5 M individual solid screening
e-Drug3D1852 FDA approved drugs between 1939 and
Super Natural II325,508 natural
CSDOver 900,000 small-molecule organic crystal
CODOver 390,000 inorganic crystals and small organic
KEGG LigandUniverse of chemical substances and
NALDBNucleic acid ligand
SMPDBOver 30,000 small molecule pathways found in
MarinChem3DOver 30,000 kinds of marine
Software of molecular docking and molecular dynamics simulations
rDockLigands against proteins and nucleic
AutoDock VinaProtein-ligand
UCSF DOCKProtein-ligand
MOE DockProtein-ligand
AmberMolecular dynamics
GromacsMolecular dynamics
NAMDMolecular dynamics
CHARMMMolecular dynamics


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