Ligand Expo
Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry.
Description
More detailed information about this field from each metasource.
Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry.
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Webpage:
http://ligand-depot.rutgers.edu/Webpage
More detailed information about this field from each metasource.
http://ligand-depot.rutgers.edu/
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence:
Name: Ligand Expo Attribution requiredLicence name
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Ligand Expo Attribution required
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
More detailed information about this field from each metasource.
http://ligand-depot.rutgers.edu/acknowledgements.html
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Ligand Depot: a data warehouse for ligands bound to macromolecules
PMID: 15059838
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
Ligand Depot: a data warehouse for ligands bound to macromolecules
PMID: 15059838
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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Ligand Depot: a data warehouse for ligands bound to macromolecules
PubMed citations: 66.
66 articles citing: Ligand Depot: a data warehouse for ligands bound to macromolecules
Global Analysis of Deep Learning Prediction Using Large-Scale In-House Kinome-Wide Profiling Data. PMID:35694454
Investigating pair distribution function use in analysis of nanocrystalline hydroxyapatite and carbonate-substituted hydroxyapatite. PMID:35510432
Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field. PMID:35352936
The SwissSimilarity 2021 Web Tool: Novel Chemical Libraries and Additional Methods for an Enhanced Ligand-Based Virtual Screening Experience. PMID:35054998
Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria. PMID:34905555
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3. PMID:34432238
Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. PMID:34159484
Universal Architectural Concepts Underlying Protein Folding Patterns. PMID:33996891
Methods for Molecular Modelling of Protein Complexes. PMID:33950384
New computational protein design methods for de novo small molecule binding sites. PMID:33017412
Machine learning classification can reduce false positives in structure-based virtual screening. PMID:32669436
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
Probabilistic identification of saccharide moieties in biomolecules and their protein complexes. PMID:32620933
Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer. PMID:31752564
Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors. PMID:31644826
Promiscuous Ligands from Experimentally Determined Structures, Binding Conformations, and Protein Family-Dependent Interaction Hotspots. PMID:31459430
Fast, efficient fragment-based coordinate generation for Open Babel. PMID:31372768
Protective role of epigallocatechin-3-gallate in NADPH oxidase-MMP2-Spm-Cer-S1P signalling axis mediated ET-1 induced pulmonary artery smooth muscle cell proliferation. PMID:30661173
Systemic neurotransmitter responses to clinically approved and experimental neuropsychiatric drugs. PMID:30410047
X-ray-Structure-Based Identification of Compounds with Activity against Targets from Different Families and Generation of Templates for Multitarget Ligand Design. PMID:30023769
Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds. PMID:29868550
Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. PMID:28233410
AceDRG: a stereochemical description generator for ligands. PMID:28177307
Validation and extraction of molecular-geometry information from small-molecule databases. PMID:28177306
Inhibition of pro-/active MMP-2 by green tea catechins and prediction of their interaction by molecular docking studies. PMID:28013477
On the importance of composite protein multiple ligand interactions in protein pockets. PMID:27864975
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. PMID:27803746
The Structure of the Periplasmic Sensor Domain of the Histidine Kinase CusS Shows Unusual Metal Ion Coordination at the Dimeric Interface. PMID:27583660
NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. PMID:27530928
Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders. PMID:27073698
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. PMID:27050687
The solvent component of macromolecular crystals. PMID:25945568
Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling. PMID:25755662
Models of protein-ligand crystal structures: trust, but verify. PMID:25665575
Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. PMID:25407367
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. PMID:25404129
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. PMID:25392418
Curation and analysis of multitargeting agents for polypharmacological modeling. PMID:25133604
AFAL: a web service for profiling amino acids surrounding ligands in proteins. PMID:25085083
Small molecule inhibitors of HCV replication from pomegranate. PMID:24958333
Drawing the PDB: Protein-Ligand Complexes in Two Dimensions. PMID:24900245
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. PMID:24848013
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. PMID:24694216
Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. PMID:24688707
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. PMID:24618344
GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes. PMID:24423161
MONA - Interactive manipulation of molecule collections. PMID:23985157
Structural basis of substrate selectivity of Δ(1)-pyrroline-5-carboxylate dehydrogenase (ALDH4A1): semialdehyde chain length. PMID:23928095
Inhibition of histo-blood group antigen binding as a novel strategy to block norovirus infections. PMID:23894462
Polypharmacology: drug discovery for the future. PMID:23272792
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
SwissSidechain: a molecular and structural database of non-natural sidechains. PMID:23104376
The human "magnesome": detecting magnesium binding sites on human proteins. PMID:23095498
PDB ligand conformational energies calculated quantum-mechanically. PMID:22303903
Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. PMID:21815173
Residue preference mapping of ligand fragments in the Protein Data Bank. PMID:21417260
Ligands in PSI structures. PMID:20944227
Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases. PMID:20554051
wwLigCSRre: a 3D ligand-based server for hit identification and optimization. PMID:19429687
Superimpose: a 3D structural superposition server. PMID:18492720
Binding MOAD, a high-quality protein-ligand database. PMID:18055497
PROCOGNATE: a cognate ligand domain mapping for enzymes. PMID:17720712
Crystallographic refinement of ligand complexes. PMID:17164531
FireDB--a database of functionally important residues from proteins of known structure. PMID:17132832
A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. PMID:17069453
SuperLigands - a database of ligand structures derived from the Protein Data Bank. PMID:15943884
Tags:
Tags
More detailed information about this field from each metasource.
chemical entity
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleic acid sequence
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
small molecule binding
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Tags
More detailed information about this field from each metasource.
chemical entity
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleic acid sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
small molecule binding
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: Ligand Expo; Ligand Expo; DOI: https://doi.org/10.25504/FAIRsharing.2ma4gq; Last edited: April 26, 2021, 2:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
chemical entity molecular interaction molecular structure nucleic acid sequence protein protein interaction small molecule small molecule binding structure
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