There is a well-recognized need of creating standard datasets for which experimental bioactivity of the ligands is already known for receptors coming from
various functional classes [197] in the research community. Availability of standard
dataset for benchmarking docking would potentially aid to spot limitations and
non-optimal parameter sets used for docking and scoring with the concerned
docking program and thereby allowing tracing and possibly fixing of issues in
earlier phases of the study. Development of benchmarking datasets for docking and
scoring has been reviewed recently [197, 198]. Primary attempts toward docking
was made by Bissantz et al., a dataset contained estrogen alpha receptor (ERa) and
Table 9 Some commonly used chemical databases
Databases
Web link
Bioactivity data
Binding activity database
https://www.bindingdb.org/
ChEMBL
https://www.ebi.ac.uk/chembldb/
NCI
https://cactus.nci.nih.gov/download/nci/
PDB bind database
http://sw16.im.med.umich.edu/databases/pdbbind/index.jsp
PubChem
https://pubchem.ncbi.nlm.nih.gov/
Patents
IBM
www-935.ibm.com/services/us/gbs/bao/siip/
SureChEMBL
www.surechembl.org
Drugs
DrugBank
www.drugbank.ca
FDA
http://fdasis.nlm.nih.gov/srs/srs.jsp
Available for vHTS
ZINC
http://zinc.docking.org
ChemSpider
http://www.chemspider.com
eMolecules
www.emolecules.com
MDL drug data report
(MDDR)
http://accelrys.com/products/collaborative-science/databases/
bioactivity-databases/mddr.html
BioPrint
http://www.cerep.fr/cerep/users/pages/ProductsServices/
bioprintservices.asp
Target specific
Pfaldb
http://pfaldb.jnu.ac.in/Malaria/homeHit.action
Mycobacterium DB
http://tbnetindia.in/
Therapeutic target database http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp
KLIFS
http://klifs.vu-compmedchem.nl/
Kinase profiling inhibitor
database
http://www.kinase-screen.mrc.ac.uk/kinase-inhibitors
Structural databases
Cambridge crystallographic
data center
https://www.ccdc.cam.ac.uk/
Crystallography open
database
http://www.crystallography.net/cod/
146
S. K. Panday and I. Ghosh
various functional classes [197] in the research community. Availability of standard
dataset for benchmarking docking would potentially aid to spot limitations and
non-optimal parameter sets used for docking and scoring with the concerned
docking program and thereby allowing tracing and possibly fixing of issues in
earlier phases of the study. Development of benchmarking datasets for docking and
scoring has been reviewed recently [197, 198]. Primary attempts toward docking
was made by Bissantz et al., a dataset contained estrogen alpha receptor (ERa) and
Table 9 Some commonly used chemical databases
Databases
Web link
Bioactivity data
Binding activity database
https://www.bindingdb.org/
ChEMBL
https://www.ebi.ac.uk/chembldb/
NCI
https://cactus.nci.nih.gov/download/nci/
PDB bind database
http://sw16.im.med.umich.edu/databases/pdbbind/index.jsp
PubChem
https://pubchem.ncbi.nlm.nih.gov/
Patents
IBM
www-935.ibm.com/services/us/gbs/bao/siip/
SureChEMBL
www.surechembl.org
Drugs
DrugBank
www.drugbank.ca
FDA
http://fdasis.nlm.nih.gov/srs/srs.jsp
Available for vHTS
ZINC
http://zinc.docking.org
ChemSpider
http://www.chemspider.com
eMolecules
www.emolecules.com
MDL drug data report
(MDDR)
http://accelrys.com/products/collaborative-science/databases/
bioactivity-databases/mddr.html
BioPrint
http://www.cerep.fr/cerep/users/pages/ProductsServices/
bioprintservices.asp
Target specific
Pfaldb
http://pfaldb.jnu.ac.in/Malaria/homeHit.action
Mycobacterium DB
http://tbnetindia.in/
Therapeutic target database http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp
KLIFS
http://klifs.vu-compmedchem.nl/
Kinase profiling inhibitor
database
http://www.kinase-screen.mrc.ac.uk/kinase-inhibitors
Structural databases
Cambridge crystallographic
data center
https://www.ccdc.cam.ac.uk/
Crystallography open
database
http://www.crystallography.net/cod/
146
S. K. Panday and I. Ghosh