ChemMine tools: an online service for analyzing and clustering small molecules

scientific article (publication date: 16 May 2011)

ChemMine tools: an online service for analyzing and clustering small molecules is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/nar/BackmanCG11
P356DOI10.1093/NAR/GKR320
P3181OpenCitations bibliographic resource ID1450384
P932PMC publication ID3125754
P698PubMed publication ID21576229
P5875ResearchGate publication ID51130566

P50authorTyler W H BackmanQ55188494
Thomas GirkeQ55473652
P2093author name stringYiqun Cao
P2860cites workHeuristics for chemical compound matching.Q51978084
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.Q52008917
Analysis and display of the size dependence of chemical similarity coefficientsQ73437528
Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficientsQ78552727
Molecular medicine. NIH dives into drug discoveryQ79151017
Chemical space and biologyQ81153866
Small Molecule Subgraph Detector (SMSD) toolkitQ21198771
From genomics to chemical genomics: new developments in KEGGQ24538628
DrugBank: a knowledgebase for drugs, drug actions and drug targetsQ24650300
ChEBI: a database and ontology for chemical entities of biological interestQ24650818
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinitiesQ24675698
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDBQ25257808
The Blue Obelisk-interoperability in chemical informaticsQ27062363
Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and BioinformaticsQ27065423
Towards interoperable and reproducible QSAR analyses: Exchange of datasetsQ27134746
Virtual Computational Chemistry Laboratory – Design and DescriptionQ27136404
Molecular structure input on the webQ27499199
ZINC--a free database of commercially available compounds for virtual screeningQ27656255
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settingsQ27861111
PubChem as a public resource for drug discoveryQ28111749
From Knowing to Controlling: A Path from Genomics to Drugs Using Small Molecule ProbesQ28190387
STITCH: interaction networks of chemicals and proteinsQ28465606
WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publicationsQ28842672
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settingsQ28842973
NIH Molecular Libraries InitiativeQ31127242
Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providersQ33259936
Systems chemical biologyQ33291103
Pybel: a Python wrapper for the OpenBabel cheminformatics toolkitQ33323081
ChemmineR: a compound mining framework for R.Q33348428
Chemical Descriptors Library (CDL): a generic, open source software library for chemical informaticsQ33370605
Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashingQ33533693
Chembench: a cheminformatics workbenchQ33708627
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structuresQ34323005
Maximum common subgraph isomorphism algorithms for the matching of chemical structuresQ35037939
The principle of complementarity: chemical versus biological spaceQ36153687
Strategies for compound selectionQ36393838
ChemBank: a small-molecule screening and cheminformatics resource databaseQ36454111
A maximum common substructure-based algorithm for searching and predicting drug-like compoundsQ37283353
Feature selection for descriptor based classification models. 2. Human intestinal absorption (HIA).Q38449880
Comparison of the NCI open database with seven large chemical structural databases.Q42652302
Enhanced CACTVS browser of the Open NCI DatabaseQ42670491
SuperDrug: a conformational drug databaseQ43567224
ChemMine. A compound mining database for chemical genomics.Q45999839
ChemDB update--full-text search and virtual chemical space.Q46257274
P275copyright licenseCreative Commons Attribution-NonCommercial 3.0 UnportedQ18810331
P6216copyright statuscopyrightedQ50423863
P433issueWeb Server issue
P407language of work or nameEnglishQ1860
P921main subjectonline serviceQ19967801
P304page(s)W486-91
P577publication date2011-05-16
P1433published inNucleic Acids ResearchQ135122
P1476titleChemMine tools: an online service for analyzing and clustering small molecules
P478volume39

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cites work (P2860)
Q90944260A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants
Q92860328A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules
Q92277777A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria
Q47213804A census of P. longum's phytochemicals and their network pharmacological evaluation for identifying novel drug-like molecules against various diseases, with a special focus on neurological disorders
Q58608784A genome-scale metabolic network alignment method within a hypergraph-based framework using a rotational tensor-vector product
Q49973010A minimalistic approach to develop new anti-apicomplexa polyamines analogs.
Q33860664A multi-fingerprint browser for the ZINC database
Q37369121A novel screen for genes associated with pheromone-induced sterility
Q34566949Aminopurine derivatives as putative SopE inhibitors
Q40469984An Integrative Drug Repurposing Pipeline: Switching Viral Drugs to Breast Cancer.
Q30713511An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data
Q92320722An insilico workflow that yields experimentally comparable inhibitors for human DiHydroOrotate DeHydrogenase
Q90800638Anti-aggregation effect on platelets of Indiplon a hypnotic sedative non-benzodiazepine drug
Q60949755Anti-flavi: A Web Platform to Predict Inhibitors of Using QSAR and Peptidomimetic Approaches
Q93178453Automated in vivo screen in zebrafish identifies Clotrimazole as targeting a metabolic vulnerability in a melanoma model
Q91165375AutophagySMDB: a curated database of small molecules that modulate protein targets regulating autophagy
Q59340718Biaryl scaffold-focused virtual screening for anti-aggregatory and neuroprotective effects in Alzheimer's disease
Q92503493Bigger Data Approach to Analysis of Essential Oils and Their Antifungal Activity against Aspergillus niger, Candida albicans, and Cryptococcus neoformans
Q90960435Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook
Q34914801Biopharmaceutical profiling of a pyrido[4,3-d] pyrimidine compound library
Q96170490Bisbenzylisoquinoline alkaloids and P-glycoprotein function: A structure activity relationship study
Q38803953C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms
Q43355113Caralluma umbellata Peroxidase: Biochemical Characterization and Its Detoxification Potentials in Comparison with Horseradish Peroxidase
Q34548103Carbamate Insecticides Target Human Melatonin Receptors
Q103822958Carnosine to Combat Novel Coronavirus (nCoV): Molecular Docking and Modeling to Cocrystallized Host Angiotensin-Converting Enzyme 2 (ACE2) and Viral Spike Protein
Q51325204ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery.
Q28597044Chemical Genetics Uncovers Novel Inhibitors of Lignification, Including p-Iodobenzoic Acid Targeting CINNAMATE-4-HYDROXYLASE
Q50890144Chemical Inhibition of Kynureninase Reduces Pseudomonas aeruginosa Quorum Sensing and Virulence Factor Expression.
Q91441006Chemical structure of semiochemicals and key binding sites together determine the olfactory functional modes of odorant-binding protein 2 in Eastern honey bee, Apis cerana
Q35059291Cheminformatic analysis of high-throughput compound screens.
Q35562890Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models
Q51312995Classification of ligand molecules in PDB with fast heuristic graph match algorithm COMPLIG.
Q38598719Comparing structural and transcriptional drug networks reveals signatures of drug activity and toxicity in transcriptional responses
Q89841268Comparison of the potential mechanisms for hepatotoxicity of p-dialkoxy chlorobenzenes in rat primary hepatocytes for read-across
Q35621076Computational modeling and biological validation of novel non-steroidal ligands for the cholesterol recognition/interaction amino acid consensus (CRAC) motif of the mitochondrial translocator protein (TSPO).
Q98305881Computational studies on bacterial secondary metabolites against breast cancer
Q54257123Computer-aided scaffold hopping to identify a novel series of casein kinase 1 delta (CK1d) inhibitors for amyotrophic lateral sclerosis.
Q92564708Cross-Reactivity to Cephalosporins and Carbapenems in Penicillin-Allergic Patients: Two Systematic Reviews and Meta-Analyses
Q53203835Current insights into computer-aided immunotherapeutic design strategies.
Q96587171D-Peptide Builder: A Web Service to Enumerate, Analyze, and Visualize the Chemical Space of Combinatorial Peptide Libraries
Q34993998Defining estrogenic mechanisms of bisphenol A analogs through high throughput microscopy-based contextual assays
Q53821060Design, synthesis, structure-activity relationships and X-ray structural studies of novel 1-oxopyrimido[4,5-c]quinoline-2-acetic acid derivatives as selective and potent inhibitors of human aldose reductase.
Q28234865Development and mining of a volatile organic compound database
Q33943741Discovering novel neuroactive drugs through high-throughput behavior-based chemical screening in the zebrafish
Q55375238Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins.
Q39504677Discovery of YopE Inhibitors by Pharmacophore-Based Virtual Screening and Docking
Q40121241Discovery of antiviral molecules for dengue: In silico search and biological evaluation
Q94499453Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products
Q96025107Distinguishing Activities in the Photodynamic Arsenals of the Pigmented Ciliates Blepharisma sinuosum Sawaya, 1940 and Blepharisma japonicum Suzuki, 1954 (Ciliophora: Heterotrichea)
Q90722338DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data
Q35551619Ensemble-based virtual screening for cannabinoid-like potentiators of the human glycine receptor α1 for the treatment of pain
Q41209870EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape
Q101163896Epigenetic compound screening uncovers small molecules for re-activation of latent HIV-1
Q92040294Evaluating the consistency of large-scale pharmacogenomic studies
Q93071393Expanding the activity spectrum of antiviral agents
Q104736756Exploiting cheminformatic and machine learning to navigate the available chemical space of potential small molecule inhibitors of SARS-CoV-2
Q91924576Exploiting ensemble learning to improve prediction of phospholipidosis inducing potential
Q47292750Exploiting the therapeutic potential of ready-to-use drugs: Repurposing antibiotics against amyloid aggregation in neurodegenerative diseases
Q99588746Expression, affinity and functional characterization of the specific binding of two putative pheromone-binding proteins in the omnivorous German cockroach Blattella germanica
Q48100910Flexible small molecular anti-estrogens with N,N-dialkylated-2,5-diethoxy-4-morpholinoaniline scaffold targets multiple estrogen receptor conformations.
Q40121034FragClust and TestClust, two informatics tools for chemical structure hierarchical clustering analysis applied to lipidomics. The example of Alzheimer's disease
Q37035959Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis.
Q101058796GraphDTA: Predicting drug-target binding affinity with graph neural networks
Q95604115GraphDTA: Predicting drug–target binding affinity with graph neural networks
Q52663452HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors.
Q28486302High content screening of a kinase-focused library reveals compounds broadly-active against dengue viruses
Q46196204High throughput selection of novel plant growth regulators: Assessing the translatability of small bioactive molecules from Arabidopsis to crops
Q89468371High-throughput Docking and Molecular Dynamics Simulations towards the Identification of Novel Peptidomimetic Inhibitors against CDC7
Q58587902High-throughput screening for selective appetite modulators: A multibehavioral and translational drug discovery strategy
Q51076268High-throughput screening of clinically approved drugs that prime polyethylenimine transfection reveals modulation of mitochondria dysfunction response improves gene transfer efficiencies.
Q91984984Hydroxyl Groups in Synthetic and Natural-Product-Derived Therapeutics: A Perspective on a Common Functional Group
Q58572061Identification of Anti-staphylococcal and Anti-biofilm Compounds by Repurposing the Medicines for Malaria Venture Pathogen Box
Q36309711Identification of C3b-Binding Small-Molecule Complement Inhibitors Using Cheminformatics.
Q88643840Identification of Compounds That Prolong Type I Interferon Signaling as Potential Vaccine Adjuvants
Q28551394Identification of New Molecular Entities (NMEs) as Potential Leads against Tuberculosis from Open Source Compound Repository
Q96950052Identification of a druggable binding pocket in the spike protein reveals a key site for existing drugs potentially capable of combating Covid-19 infectivity
Q92648725Identification of new DNA gyrase inhibitors based on bioactive compounds from streptomyces: structure-based virtual screening and molecular dynamics simulations approaches
Q28828721Identification of novel bacterial DNA gyrase inhibitors: An in silico study
Q28534763Identification of novel compounds inhibiting chikungunya virus-induced cell death by high throughput screening of a kinase inhibitor library
Q36120652Identification of pyrrolo[3,2-c]pyridin-4-amine compounds as a new class of entry inhibitors against influenza viruses in vitro
Q36394668Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques
Q35007796Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism
Q64092935ImmtorLig_DB: repertoire of virtually screened small molecules against immune receptors to bolster host immunity
Q90471370Implementation of a Pipeline Using Disease-Disease Associations for Computational Drug Repurposing
Q57037794In Silico Identification of JMJD3 Demethylase Inhibitors
Q89470046In silico identification of potential inhibitors against human 2'-5'- oligoadenylate synthetase (OAS) proteins
Q98509890In silico methods predict new blood-brain barrier permeable structure for the inhibition of kynurenine 3-monooxygenase
Q41009995Informatic search strategies to discover analogues and variants of natural product archetypes.
Q90289854Innovations in improving lipid production: Algal chemical genetics
Q92092467Insights about multi-targeting and synergistic neuromodulators in Ayurvedic herbs against epilepsy: integrated computational studies on drug-target and protein-protein interaction networks
Q47857752Investigation of novel pharmacological chaperones for Gaucher Disease.
Q104742250Is clay-polycation adsorbent future of the greener society? In silico modeling approach with comprehensive virtual screening
Q30669298Ligand binding studies, preliminary structure-activity relationship and detailed mechanistic characterization of 1-phenyl-6,6-dimethyl-1,3,5-triazine-2,4-diamine derivatives as inhibitors of Escherichia coli dihydrofolate reductase
Q57149828Lipid-Based Oral Formulation Strategies for Lipophilic Drugs
Q61818383Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets
Q92633790Machine-Learning-Assisted De Novo Design of Organic Molecules and Polymers: Opportunities and Challenges
Q28597594MetMaxStruct: A Tversky-Similarity-Based Strategy for Analysing the (Sub)Structural Similarities of Drugs and Endogenous Metabolites
Q94556398Metagenomic Insight Towards Vanillin-Mediated Membrane Biofouling Prevention: In Silico Docking Validation
Q50020529Molecular Insights into Function and Competitive Inhibition of Pseudomonas aeruginosa Multiple Virulence Factor Regulator.
Q52809378New potential inhibitors of mTOR: a computational investigation integrating molecular docking, virtual screening and molecular dynamics simulation.
Q91296030Non-sedating benzodiazepines cause paralysis and tissue damage in the parasitic blood fluke Schistosoma mansoni
Q34156744Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery
Q91747800Novel Salicylic Acid Analogs Induce a Potent Defense Response in Arabidopsis
Q92659210Novel narrow spectrum benzyl thiophene sulfonamide derivatives to control Campylobacter
Q42675058Novel pH-Stable Glycoside Hydrolase Family 3 β-Xylosidase from Talaromyces amestolkiae: an Enzyme Displaying Regioselective Transxylosylation.
Q89576403Novel pyrazine based anti-tubercular agents: Design, synthesis, biological evaluation and in silico studies
Q40241810ONRLDB--manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery.
Q38119805One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade
Q28833683Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events
Q21198766Open Babel: An open chemical toolbox
Q57832760Open chemoinformatic resources to explore the structure, properties and chemical space of molecules
Q28486122Phosphoinositide 3-kinase dependent inhibition as a broad basis for opponent coding in Mammalian olfactory receptor neurons
Q38664956Platform for Unified Molecular Analysis: PUMA.
Q29048210Prediction of the permeability of neutral drugs inferred from their solvation properties
Q34345049Pregnane X receptor and drug-induced liver injury.
Q94571401Protection against peripheral artery disease injury by Ruan Jian Qing mai formula via metabolic programming
Q34615684PubChem applications in drug discovery: a bibliometric analysis
Q39411779Review and analysis of FDA approved drugs using lipid-based formulations.
Q38491740SMMRNA: a database of small molecule modulators of RNA.
Q35686324Screen of FDA-approved drug library identifies maprotiline, an antibiofilm and antivirulence compound with QseC sensor-kinase dependent activity in Francisella novicida
Q35470873Screening of a chemical library reveals novel PXR-activating pharmacologic compounds
Q92997542Screening of novel histone deacetylase 7 inhibitors through molecular docking followed by a combination of molecular dynamics simulations and ligand-based approach
Q36316477Shared Ligands Between Organic Anion Transporters (OAT1 and OAT6) and Odorant Receptors
Q55188697Shining Light on Molecular Mechanism for Odor-selectivity of CNT-immobilized Olfactory Receptor.
Q37992129Small molecules present large opportunities in plant biology
Q100559100Statistical models for identifying frequent hitters in high throughput screening
Q57039721Statistical recipe for quantifying microbial functional diversity from EcoPlate metabolic profiling
Q89767298Striking essential oil: tapping into a largely unexplored source for drug discovery
Q30399603Structural Evaluation and Binding Mode Analysis of CCL19 and CCR7 Proteins-Identification of Novel Leads for Rheumatic and Autoimmune Diseases: An Insilico study
Q88905871Structural insights into pharmacophore-assisted in silico identification of protein-protein interaction inhibitors for inhibition of human toll-like receptor 4 - myeloid differentiation factor-2 (hTLR4-MD-2) complex
Q93333339Structurally unique PARP-1 inhibitors for the treatment of prostate cancer
Q47872719Structure-activity relationships among DNA ligase inhibitors: Characterization of a selective uncompetitive DNA ligase I inhibitor
Q36057287Structure-based virtual screening of hypothetical inhibitors of the enzyme longiborneol synthase-a potential target to reduce Fusarium head blight disease.
Q36210915Structure-performance relationships of phenyl cinnamic acid derivatives as MALDI-MS matrices for sulfatide detection
Q47396402Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders
Q94524544Synergistic and antagonistic drug interactions in the treatment of systemic fungal infections
Q92660432Synthesis and biological evaluation of indole-2-carbohydrazides and thiazolidinyl-indole-2-carboxamides as potent tubulin polymerization inhibitors
Q40885312Synthesis of novel coumarin appended bis(formylpyrazole) derivatives: Studies on their antimicrobial and antioxidant activities
Q104110490Synthesis, biological evaluation and QSAR studies of new thieno[2,3-d]pyrimidin-4(3H)-one derivatives as antimicrobial and antifungal agents
Q93184593Target Identification Using Homopharma and Network-Based Methods for Predicting Compounds Against Dengue Virus-Infected Cells
Q89362707Targeting a hidden site on class A beta-lactamases
Q46324496Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening
Q99213377Targeting the Initiator Protease of the Classical Pathway of Complement Using Fragment-Based Drug Discovery
Q60915016The (R)-enantiomer of the 6-chromanol derivate SUL-121 improves renal graft perfusion via antagonism of the α-adrenoceptor
Q61800932The Distribution of Standard Deviations Applied to High Throughput Screening
Q28830661The Small Molecule Hyperphyllin Enhances Leaf Formation Rate and Mimics Shoot Meristem Integrity Defects Associated with AMP1 Deficiency
Q59341209The Varieties of the Psychedelic Experience: A Preliminary Study of the Association Between the Reported Subjective Effects and the Binding Affinity Profiles of Substituted Phenethylamines and Tryptamines
Q39029268The effects of iron limitation and cell density on prokaryotic metabolism and gene expression: Excerpts from Fusobacterium necrophorum strain 774 (sheep isolate).
Q50128380The in silico drug discovery toolbox: applications in lead discovery and optimization.
Q91275948The many dimensions of phytochemical diversity: linking theory to practice
Q68414290The metaRbolomics Toolbox in Bioconductor and beyond
Q94317027The rcdk and cluster R packages applied to drug candidate selection
Q94487529The yeast (Saccharomyces cerevisiae) YCF1 vacuole transporter: Evidence on its implication into the yeast resistance to flusilazole as revealed by GC/EI/MS metabolomics
Q54376606Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 1. Database Development and Analysis
Q47617340Up in Smoke: Uncovering a Lack of Evidence for Proton Pump Inhibitors as a Source of Tetrahydrocannibol Immunoassay False Positives
Q90427802Using MS-FINDER for identifying 19 natural products in the CASMI 2016 contest
Q44201372Virtual screening approach to identifying influenza virus neuraminidase inhibitors using molecular docking combined with machine-learning-based scoring function
Q36538579Virtual screening of specific insulin-like growth factor 1 receptor (IGF1R) inhibitors from the National Cancer Institute (NCI) molecular database
Q90428394Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace
Q27902306Visual analytics in cheminformatics: user-supervised descriptor selection for QSAR methods
Q27010340Web tools for predictive toxicology model building
Q48107835WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces
Q41597054Xeronine structure and function: computational comparative mastery of its mystery.
Q34365383fmcsR: mismatch tolerant maximum common substructure searching in R.
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