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Databases and Softwares

Macromolecular structure databases
Structure databasesDescriptionWeblink
wwPDBWorldwide macromolecular structureswww.wwpdb.org
RCSB PDBMacromolecular structureswww.rcsb.org
PDBeMacromolecular structures in Europewww.ebi.ac.uk/pdbe
PDBjMacromolecular structures in Japanpdbj.org
BMRBMacromolecular structures from NMRwww.bmrb.wisc.edu
NDBNucleic acid structure databasendbserver.rutgers.edu
MMDB3D macromolecular structureswww.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml
JenaLib3D biopolymer structuresjenalib.leibniz-fli.de
PDBbind3D macromolecular structures in complex with ligandswww.pdbbind.org.cn
IUPHAR/BPS Guide to PHARMACOLOGYPharmacological targets and substanceswww.guidetopharmacology.org
ModBaseTheoretical 3D macromolecular structuresmodbase.compbio.ucsf.edu/modbase-cgi/index.cgi
PMPTheoretical 3D macromolecular structureswww.proteinmodelportal.org
SWISS-MODELTheoretical 3D macromolecular structuresswissmodel.expasy.org/repository
Small molecule databases
Ligand databasesDescriptionWeblink
ZINCOver 35 million purchasable compounds for virtual screeningzinc.docking.org
PubChemOver 90 million compoundspubchem.ncbi.nlm.nih.gov
DrugBankMore than 11,000 drug entrieswww.drugbank.ca
SpecsProviding high throughput screening compoundswww.specs.net
ChemBridgeOver 1.1 million druglike and leadlike compoundswww.chembridge.com/screening_libraries
ChemDivOver 1,5 M individual solid screening compoundswww.chemdiv.com/services-menu/screening-libraries
e-Drug3D1852 FDA approved drugs between 1939 and 2017chemoinfo.ipmc.cnrs.fr/MOLDB/index.html
Super Natural II325,508 natural compoundsbioinf-applied.charite.de/supernatural_new/index.php
CSDOver 900,000 small-molecule organic crystal structureswww.ccdc.cam.ac.uk/solutions/csd-system/components/csd
CODOver 390,000 inorganic crystals and small organic compoundswww.crystallography.net/cod
KEGG LigandUniverse of chemical substances and reactionswww.genome.jp/kegg/ligand.html
NALDBNucleic acid ligand databasebsbe.iiti.ac.in/bsbe/naldb/HOME.php
SMPDBOver 30,000 small molecule pathways found in humanssmpdb.ca
MarinChem3DOver 30,000 kinds of marine compoundsmc3d.qnlm.ac
Software of molecular docking and molecular dynamics simulations
SoftwareDescriptionWeblink
LeDockProtein-ligand dockingwww.lephar.com/software.htm
rDockLigands against proteins and nucleic acidsrdock.sourceforge.net
AutoDockProtein-ligand dockingautodock.scripps.edu
AutoDock VinaProtein-ligand dockingvina.scripps.edu
UCSF DOCKProtein-ligand dockingdock.compbio.ucsf.edu
LigandFitProtein-ligand dockingaccelrys.com
GlideProtein-ligand dockingwww.schrodinger.com
GOLDProtein-ligand dockingwww.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold
MOE DockProtein-ligand dockingwww.chemcomp.com
Surflex-DockProtein-ligand dockingwww.jainlab.org
AmberMolecular dynamics simulationsambermd.org
GromacsMolecular dynamics simulationswww.gromacs.org
NAMDMolecular dynamics simulationswww.ks.uiuc.edu/Research/namd
CHARMMMolecular dynamics simulationswww.charmm.org
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