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Ligand Expo specifications

Information


Unique identifier OMICS_02751
Name Ligand Expo
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Ligand Expo Team

Publication for Ligand Expo

Ligand Expo citations

 (11)
library_books

ForceGen 3D structure and conformer generation: from small lead like molecules to macrocyclic drugs

2017
J Comput Aided Mol Des
PMCID: 5429375
PMID: 28289981
DOI: 10.1007/s10822-017-0015-8

[…] igand is retained. Structure match to alternate curation Graph matching is done between the final ligand and the corresponding SMILES-based molecular structure (and tautomeric variants) from the RCSB Ligand Expo. If there is a match, the ligand is retained. In a few cases where a ligand from a reported benchmark failed this process, manual adjustment of bond orders was done (this was needed for se […]

library_books

The polypharmacology browser: a web based multi fingerprint target prediction tool using ChEMBL bioactivity data

2017
J Cheminform
PMCID: 5319934
PMID: 28270862
DOI: 10.1186/s13321-017-0199-x

[…] ormat. An option is available to extract the query molecule from the Protein Data Bank (PDB) using the PDB id of the protein–ligand complex of interest (the PDB ligand data was downloaded from http://ligand-expo.rcsb.org/ website in March 2016 and stored on our web server, and will be updated once a year). The option “No. of targets” allows the user to input the number of targets to be returned by […]

call_split

Predicting Ligand Binding Sites on Protein Surfaces by 3 Dimensional Probability Density Distributions of Interacting Atoms

2016
PLoS One
PMCID: 4981321
PMID: 27513851
DOI: 10.1371/journal.pone.0160315
call_split See protocol

[…] d atom distribution database was derived from 17023 known protein-ligand complex structures (S17023 dataset) released before Aug/2014. These complex structures were obtained from PDB web site: http://ligand-expo.rcsb.org/dictionaries/cc-to-pdb.tdd. 30% sequence identity threshold was used to remove structure redundancy among structures binding to the same ligand. In addition, structures that satis […]

library_books

Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders

2016
PMCID: 4814692
PMID: 27073698
DOI: 10.1155/2016/6378137

[…] In addition to the NIMH PDSP database, other chemical databases are available. For example, Ligand Expo [], ZINC [], and KEGG DRUG [] databases integrate diverse information such as molecular pathways, binding experiments, and drug targets. One of the large public databases, PubChem, contain […]

call_split

Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis

2016
Sci Rep
PMCID: 4726147
PMID: 26805589
DOI: 10.1038/srep19681
call_split See protocol

[…] f HsQPRT-QA or HsQPRT-NAMN were obtained by molecular replacement with Phaser using the HsQPRT-tartrate complex as a template. Coordinates of nine QA and twelve NAMN molecules were obtained from RCSB Ligand Expo (http://ligand-expo.rcsb.org) and placed into the density corresponds to them. Multiple rounds of refinement were performed using REFMAC5 to final 2.8 (apo), 3.1 (HsQPRT-QA) and 2.6 (HsQPR […]

library_books

Curation and Analysis of Multitargeting Agents for Polypharmacological Modeling

2014
J Chem Inf Model
PMCID: 4170814
PMID: 25133604
DOI: 10.1021/ci500092j

[…] insights for off-target identification and polypharmacological agent design. A flowchart illustrating the data curation is provided in Figure . The curation was started by obtaining ligand data from Ligand Expo, and their interactions with targets were analyzed based on their crystal structures in the PDB. As of March 10, 2013, the Ligand Expo contained 15,952 small molecules which were included […]

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Ligand Expo institution(s)
Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA

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