Macromolecular structure databases | ||
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Structure databases | Description | Weblink |
wwPDB | Worldwide macromolecular structures | www.wwpdb.org |
RCSB PDB | Macromolecular structures | www.rcsb.org |
PDBe | Macromolecular structures in Europe | www.ebi.ac.uk/pdbe |
PDBj | Macromolecular structures in Japan | pdbj.org |
BMRB | Macromolecular structures from NMR | www.bmrb.wisc.edu |
NDB | Nucleic acid structure database | ndbserver.rutgers.edu |
MMDB | 3D macromolecular structures | www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml |
JenaLib | 3D biopolymer structures | jenalib.leibniz-fli.de |
PDBbind | 3D macromolecular structures in complex with ligands | www.pdbbind.org.cn |
IUPHAR/BPS Guide to PHARMACOLOGY | Pharmacological targets and substances | www.guidetopharmacology.org |
ModBase | Theoretical 3D macromolecular structures | modbase.compbio.ucsf.edu/modbase-cgi/index.cgi |
PMP | Theoretical 3D macromolecular structures | www.proteinmodelportal.org |
SWISS-MODEL | Theoretical 3D macromolecular structures | swissmodel.expasy.org/repository |
Small molecule databases | ||
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Ligand databases | Description | Weblink |
ZINC | Over 35 million purchasable compounds for virtual screening | zinc.docking.org |
PubChem | Over 90 million compounds | pubchem.ncbi.nlm.nih.gov |
DrugBank | More than 11,000 drug entries | www.drugbank.ca |
Specs | Providing high throughput screening compounds | www.specs.net |
ChemBridge | Over 1.1 million druglike and leadlike compounds | www.chembridge.com/screening_libraries |
ChemDiv | Over 1,5 M individual solid screening compounds | www.chemdiv.com/services-menu/screening-libraries |
e-Drug3D | 1852 FDA approved drugs between 1939 and 2017 | chemoinfo.ipmc.cnrs.fr/MOLDB/index.html |
Super Natural II | 325,508 natural compounds | bioinf-applied.charite.de/supernatural_new/index.php |
CSD | Over 900,000 small-molecule organic crystal structures | www.ccdc.cam.ac.uk/solutions/csd-system/components/csd |
COD | Over 390,000 inorganic crystals and small organic compounds | www.crystallography.net/cod |
KEGG Ligand | Universe of chemical substances and reactions | www.genome.jp/kegg/ligand.html |
NALDB | Nucleic acid ligand database | bsbe.iiti.ac.in/bsbe/naldb/HOME.php |
SMPDB | Over 30,000 small molecule pathways found in humans | smpdb.ca |
MarinChem3D | Over 30,000 kinds of marine compounds | mc3d.qnlm.ac |
Software of molecular docking and molecular dynamics simulations | ||
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Software | Description | Weblink |
LeDock | Protein-ligand docking | www.lephar.com/software.htm |
rDock | Ligands against proteins and nucleic acids | rdock.sourceforge.net |
AutoDock | Protein-ligand docking | autodock.scripps.edu |
AutoDock Vina | Protein-ligand docking | vina.scripps.edu |
UCSF DOCK | Protein-ligand docking | dock.compbio.ucsf.edu |
LigandFit | Protein-ligand docking | accelrys.com |
Glide | Protein-ligand docking | www.schrodinger.com |
GOLD | Protein-ligand docking | www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold |
MOE Dock | Protein-ligand docking | www.chemcomp.com |
Surflex-Dock | Protein-ligand docking | www.jainlab.org |
Amber | Molecular dynamics simulations | ambermd.org |
Gromacs | Molecular dynamics simulations | www.gromacs.org |
NAMD | Molecular dynamics simulations | www.ks.uiuc.edu/Research/namd |
CHARMM | Molecular dynamics simulations | www.charmm.org |
Services