A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery

A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery is …
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scholarly articleQ13442814

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P6179Dimensions Publication ID1169013376
P356DOI10.1021/ACSCENTSCI.3C00800
P953full work available at URLhttps://pubs.acs.org/doi/pdf/10.1021/acscentsci.3c00800
P10283OpenAlex IDW4391957298
P932PMC publication ID10979503
P8299Semantic Scholar corpus ID263313465
P4011Semantic Scholar paper ID01d0cc4b77304c1f974ff0db2b8f096586488d09

P7228access restriction statusopen accessQ232932
P7137acknowledgedFederal Ministry of Education and ResearchQ492234
Laboratoires Pierre FabreQ626597
Ministry of Foreign Affairs of the NetherlandsQ1037495
Drugs for Neglected Diseases InitiativeQ2717504
P50authorAntonio GrondinQ116245496
Jean-Robert IosetQ124670633
Marcel KaiserQ30347237
Luis Quirós-GuerreroQ104071610
Bruno DavidQ110950839
Jean-Luc WolfenderQ56084663
Pierre-Marie AllardQ56451301
Florence MehlQ58856504
Emerson Ferreira QueirozQ87644493
Luca CappellettiQ95661345
Adriano RutzQ97455964
Sébastien MorettiQ42233018
Laurence MarcourtQ43275441
Marco PagniQ47097366
Arnaud GaudryQ55085984
P2860cites workMEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse DatasetsQ111601978
The LOTUS initiative for open knowledge management in natural products researchQ112143478
Toward better drug discovery with knowledge graphQ112819362
matchms - processing and similarity evaluation of mass spectrometry data.Q113307511
Mass spectrometry data on specialized metabolome of medicinal plants used in East Asian traditional medicineQ113633132
Database-independent molecular formula annotation using Gibbs sampling through ZODIACQ114864640
Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019Q114867582
CFM-ID 4.0: More Accurate ESI-MS/MS Spectral Prediction and Compound IdentificationQ114871623
Universal Spectrum Identifier for mass spectraQ114953382
Isolation and characterization of pristimerin as the antiplasmodial and antileishmanial agent of Maytenus senegalensis (Lam.) Exell.Q115949731
Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extractsQ116245417
Trapping‐Enrichment Multi‐dimensional Liquid Chromatography with On‐Line Deuterated Solvent Exchange for Streamlined Structure Elucidation at the Microgram ScaleQ127060110
A NEW FLUOROMETRIC ASSAY FOR CYTOTOXICITY MEASUREMENTS IN-VITROQ127060112
Trackable and scalable LC-MS metabolomics data processing using asariQ127060119
lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotationQ127060120
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguationQ127060122
Cultivation in a semi-defined medium of animal infective forms of Trypanosoma brucei, T. equiperdum, T. evansi, T. rhodesiense and T. gambiense.Q128791915
Synthesis of phylogeny and taxonomy into a comprehensive tree of lifeQ21714372
Cytoscape: a software environment for integrated models of biomolecular interaction networksQ24515682
A cross-platform toolkit for mass spectrometry and proteomicsQ24629036
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile dataQ27136473
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysisQ27807488
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular NetworkingQ27818844
ClassyFire: automated chemical classification with a comprehensive, computable taxonomyQ27902281
ChEMBL: a large-scale bioactivity database for drug discoveryQ28315179
ChEMBL web services: streamlining access to drug discovery data and utilitiesQ28647641
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identificationQ29616057
Mass spectral molecular networking of living microbial coloniesQ30519465
Pure compound libraries; a new perspective for natural product based drug discoveryQ30699667
ReDU: a framework to find and reanalyze public mass spectrometry dataQ98513836
Feature-based molecular networking in the GNPS analysis environmentQ98665248
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectraQ102369470
Studies on terpenoids and steroids. Part 10. Structures of four new natural phenol is D:A-friedo-24-noroleanane triterpenoidsQ104393001
Visualization of very large high-dimensional data sets as minimum spanning treesQ106856815
UMAP: Uniform Manifold Approximation and ProjectionQ107272666
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationshipsQ108126799
Advancements in capturing and mining mass spectrometry data are transforming natural products researchQ108844055
High-confidence structural annotation of metabolites absent from spectral librariesQ109715913
NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural ProductsQ110391628
OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of LifeQ111149904
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browserQ111441830
A knowledge graph to interpret clinical proteomics dataQ111509846
The pharmaceutical industry and natural products: historical status and new trendsQ58856029
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure informationQ63352058
Wikidata: A large-scale collaborative ontological medical databaseQ68471881
Respiratory control in mitochondria from Trypanosoma cruziQ69914799
Rotenone at high concentrations inhibits NADH-fumarate reductase and the mitochondrial respiratory chain of Trypanosoma brucei and T. cruziQ74773675
Potentially cytotoxic triterpenoids from the root bark of Siphonodon celastrineus GriffQ81882965
Wikidata as a knowledge graph for the life sciencesQ87830400
Cytotoxic Triterpenes from Salacia crassifolia and Metabolite Profiling of Celastraceae SpeciesQ89170532
Troubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big CohortsQ90946288
Taxonomically Informed Scoring Enhances Confidence in Natural Products AnnotationQ91218352
Innovative omics-based approaches for prioritisation and targeted isolation of natural products - new strategies for drug discoveryQ91903041
Mass spectrometry searches using MASSTQ92365644
Utility of dry load injection for an efficient natural products isolation at the semi-preparative chromatographic scaleQ92705165
Plate-based diversity selection based on empirical HTS data to enhance the number of hits and their chemical diversityQ33468796
Property distributions: differences between drugs, natural products, and molecules from combinatorial chemistryQ34172646
Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profilesQ34279373
Efficient technique for screening drugs for activity against Trypanosoma cruzi using parasites expressing beta-galactosidaseQ35129381
Cheminformatic comparison of approved drugs from natural product versus synthetic originsQ36167128
Searching molecular structure databases with tandem mass spectra using CSI:FingerID.Q36179301
Bioactive natural products prioritization using massive multi-informational molecular networksQ38614529
One Step Forward for Reducing False Positive and False Negative Compound Identifications from Mass Spectrometry Metabolomics Data: New Algorithms for Constructing Extracted Ion Chromatograms and Detecting Chromatographic Peaks.Q38655770
Chemical constituents from Waltheria indica exert in vitro activity against Trypanosoma brucei and T. cruzi.Q38864380
A comparison of three methods of estimating EC50 in studies of drug resistance of malaria parasitesQ39085081
The Alamar Blue® assay to determine drug sensitivity of African trypanosomes (T.b. rhodesiense and T.b. gambiense) in vitroQ39416311
Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication.Q39993461
Antifungal Quinoline Alkaloids from Waltheria indicaQ40020934
A new rapid and simple non-radioactive assay to monitor and determine the proliferation of lymphocytes: an alternative to [3H]thymidine incorporation assayQ41474027
Systematic integration of biomedical knowledge prioritizes drugs for repurposingQ42255083
Bisnortriterpenes from Salacia madagascariensisQ43948141
Antiprotozoal activity of quinonemethide triterpenes from Maytenus ilicifolia (Celastraceae).Q46081991
A simple colorimetric method to screen drug cytotoxicity against Leishmania using the dye Alamar BlueQ50506555
Natural product-likeness score and its application for prioritization of compound librariesQ51899910
New culture medium for maintenance of tsetse tissues and growth of trypanosomatidsQ52434329
Propagating annotations of molecular networks using in silico fragmentationQ52580602
Sachem: a chemical cartridge for high-performance substructure search.Q55016200
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P4510describes a project that usesWikidataQ2013
liquid chromatography–mass spectrometryQ873864
ChEMBLQ6120337
RDFLibQ7276224
NMR spectroscopyQ10359898
PythonQ28865
NPClassifierQ112144253
MZmineQ112189098
msConvertQ112506514
SIRIUSQ124358188
Semantic WebQ54837
Open Tree of LifeQ22661281
LOTUSQ104225190
Ontotext GraphDBQ58425577
P8324funderSwiss National Science FoundationQ471732
P407language of work or nameEnglishQ1860
P921main subjectdata miningQ172491
software frameworkQ271680
liquid chromatography–mass spectrometryQ873864
natural productQ901227
drug discoveryQ1418791
Pristimera indicaQ11075650
Reissantia indicaQ17240574
bioactive compoundQ17774539
11β-hydroxypristimerinQ125208651
celastrol methyl esterQ27108073
ZeylasteralQ105027438
knowledge graphQ33002955
P6954online access statusopen accessQ232932
P577publication date2024-02-20
P1433published inACS Central ScienceQ27726586
P1476titleA Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery

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