ADME prediction with KNIME: In silico aqueous solubility consensus model based on supervised recursive random forest approaches.
PMID:35300309
Natural product drug discovery in the artificial intelligence era.
PMID:35282622
From Platform to Knowledge Graph: Evolution of Laboratory Automation.
PMID:35252980
Naturally occurring plant-based anticancerous candidates as prospective ABCG2 inhibitors: an in silico drug discovery study.
PMID:35224675
Exploring Toxins for Hunting SARS-CoV-2 Main Protease Inhibitors: Molecular Docking, Molecular Dynamics, Pharmacokinetic Properties, and Reactome Study.
PMID:35215266
MetAMDB: Metabolic Atom Mapping Database.
PMID:35208198
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.
PMID:35183110
Good Reporting Practice for Thermophysical and Thermochemical Property Measurements (IUPAC Technical Report).
PMID:34924633
Data Centric Molecular Analysis and Evaluation of Hepatocellular Carcinoma Therapeutics Using Machine Intelligence-Based Tools.
PMID:34910274
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032.
PMID:34867870
MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data.
PMID:34822401
Perspectives on automated composition of workflows in the life sciences.
PMID:34804501
Rhea, the reaction knowledgebase in 2022.
PMID:34755880
mapMECFS: a portal to enhance data discovery across biological disciplines and collaborative sites.
PMID:34749736
High-throughput virtual screening for organic electronics: a comparative study of alternative strategies.
PMID:34745630
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra.
PMID:34715914
Predicting compound amenability with liquid chromatography-mass spectrometry to improve non-targeted analysis.
PMID:34648052
Individual and collective human intelligence in drug design: evaluating the search strategy.
PMID:34635158
Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier.
PMID:34620215
Data Ecosystems for Scientific Experiments: Managing Combustion Experiments and Simulation Analyses in Chemical Engineering.
PMID:34604739
Representation of molecules for drug response prediction.
PMID:34571534
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.
PMID:34570771
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review.
PMID:34445667
Non-β-Lactam Allosteric Inhibitors Target Methicillin-Resistant Staphylococcus aureus: An In Silico Drug Discovery Study.
PMID:34438984
DECIMER 1.0: deep learning for chemical image recognition using transformers.
PMID:34404468
Exploring Chemical Information in PubChem.
PMID:34370395
Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases.
PMID:34209357
Discovery of Novel Chemical Series of OXA-48 β-Lactamase Inhibitors by High-Throughput Screening.
PMID:34202402
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus.
PMID:34188046
Retrosynthetic accessibility score (RAscore) - rapid machine learned synthesizability classification from AI driven retrosynthetic planning.
PMID:34164104
Predicting retrosynthetic pathways using transformer-based models and a hyper-graph exploration strategy.
PMID:34122839
Plant Lipid Databases.
PMID:34047992
InChI version 1.06: now more than 99.99% reliable.
PMID:34030732
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.
PMID:33945539
Assessing the calibration in toxicological in vitro models with conformal prediction.
PMID:33926567
STOUT: SMILES to IUPAC names using neural machine translation.
PMID:33906675
Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity.
PMID:33850714
The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository.
PMID:33808985
Open, High-Resolution EI+ Spectral Library of Anthropogenic Compounds.
PMID:33768085
Teaching Cheminformatics through a Collaborative Intercollegiate Online Chemistry Course (OLCC).
PMID:33762777
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification.
PMID:33726837
Identifying New/Emerging Psychoactive Substances at the Time of COVID-19; A Web-Based Approach.
PMID:33633599
Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes.
PMID:33573096
Human Milk-Fed Piglets Have a Distinct Small Intestine and Circulatory Metabolome Profile Relative to That of Milk Formula-Fed Piglets.
PMID:33563783
The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case.
PMID:33530604
Enabling High-Throughput Searches for Multiple Chemical Data Using the U.S.-EPA CompTox Chemicals Dashboard.
PMID:33481596
An open source chemical structure curation pipeline using RDKit.
PMID:33431044
Molecular representations in AI-driven drug discovery: a review and practical guide.
PMID:33431035
Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES.
PMID:33431026
GEN: highly efficient SMILES explorer using autodidactic generative examination networks.
PMID:33430998
Dataset's chemical diversity limits the generalizability of machine learning predictions.
PMID:33430991
COVER: conformational oversampling as data augmentation for molecules.
PMID:33430975
Editorial for the Special Issue From Nanoinformatics to Nanomaterials Risk Assessment and Governance.
PMID:33430326
patRoon: open source software platform for environmental mass spectrometry based non-target screening.
PMID:33407901
Chemical graph generators.
PMID:33400699
Chemoinformatics-based enumeration of chemical libraries: a tutorial.
PMID:33372622
Neonatal Diet Impacts the Large Intestine Luminal Metabolome at Weaning and Post-Weaning in Piglets Fed Formula or Human Milk.
PMID:33365033
MET: a Java package for fast molecule equivalence testing.
PMID:33334379
Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?
PMID:33322568
NPBS database: a chemical data resource with relational data between natural products and biological sources.
PMID:33306802
ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding.
PMID:33292568
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning.
PMID:33292482
REDIAL-2020: A Suite of Machine Learning Models to Estimate Anti-SARS-CoV-2 Activities.
PMID:33200119
PubChem in 2021: new data content and improved web interfaces.
PMID:33151290
Generating Multibillion Chemical Space of Readily Accessible Screening Compounds.
PMID:33145486
Global Substance Registration System: consistent scientific descriptions for substances related to health.
PMID:33137173
Best Practices for Making Reproducible Biochemical Models.
PMID:32853539
Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells.
PMID:32759214
HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs.
PMID:32746900
A Pilot Study of Multi-Input Recurrent Neural Networks for Drug-Kinase Binding Prediction.
PMID:32722290
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources.
PMID:32429287
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks.
PMID:32423472
Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry.
PMID:32385318
BioHackathon 2015: Semantics of data for life sciences and reproducible research.
PMID:32308977
Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model.
PMID:32231124
Improving lipid mapping in Genome Scale Metabolic Networks using ontologies.
PMID:32215752
Striking essential oil: tapping into a largely unexplored source for drug discovery.
PMID:32071337
Atomic structures and orbital energies of 61,489 crystal-forming organic molecules.
PMID:32071311
Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2.
PMID:32043883
Heritability estimates for 361 blood metabolites across 40 genome-wide association studies.
PMID:31911595
Experiment design driven FAIRification of omics data matrices, an exemplar.
PMID:31831744
BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities.
PMID:31783634
Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial Pharmaceutical Research.
PMID:31749705
Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics.
PMID:31717785
TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration.
PMID:31680154
Perspective isomorphs - a new classification of molecular structures based on artistic and chemical concepts.
PMID:31666866
DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data.
PMID:31614716
The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation.
PMID:31579352
BigSMILES: A Structurally-Based Line Notation for Describing Macromolecules.
PMID:31572779
The metaRbolomics Toolbox in Bioconductor and beyond.
PMID:31548506
Workflows Allowing Creation of Journal Article Supporting Information and Findable, Accessible, Interoperable, and Reusable (FAIR)-Enabled Publication of Spectroscopic Data.
PMID:31459544
PUG-View: programmatic access to chemical annotations integrated in PubChem.
PMID:31399858
AqSolDB, a curated reference set of aqueous solubility and 2D descriptors for a diverse set of compounds.
PMID:31395888
Improving MetFrag with statistical learning of fragment annotations.
PMID:31277571
Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking.
PMID:31257108
A fully computational and reasonable representation for karyotypes.
PMID:31228194
Identification of compounds that rescue otic and myelination defects in the zebrafish adgrg6 (gpr126) mutant.
PMID:31180326
The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis.
PMID:31178829
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity.
PMID:31152262
Catalysis-Hub.org, an open electronic structure database for surface reactions.
PMID:31138816
Navigating in vitro bioactivity data by investigating available resources using model compounds.
PMID:31036807
DNAmod: the DNA modification database.
PMID:31016417
Free Accessible Databases as a Source of Information about Food Components and Other Compounds with Anticancer Activity⁻Brief Review.
PMID:30813234
Automated evaluation of consistency within the PubChem Compound database.
PMID:30778259
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling.
PMID:30736318
A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications.
PMID:30536051
A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae).
PMID:30498089
ChEMBL: towards direct deposition of bioassay data.
PMID:30398643
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations.
PMID:30246165
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.
PMID:30084866
Designing Algorithms To Aid Discovery by Chemical Robots.
PMID:30062108
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results.
PMID:29982278
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center.
PMID:29917015
Collaboration of the Joint Research Centre and European Customs Laboratories for the Identification of New Psychoactive Substances.
PMID:29792142
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database.
PMID:29777317
MetExplore: collaborative edition and exploration of metabolic networks.
PMID:29718355
NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.
PMID:29656574
Caveat Usor: Assessing Differences between Major Chemistry Databases.
PMID:29451740
Strategies for dereplication of natural compounds using high-resolution tandem mass spectrometry.
PMID:29225718
RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions.
PMID:29220456
Demonstration of a consensus approach for the calculation of physicochemical properties required for environmental fate assessments.
PMID:29197820
Annotation of Peptide Structures Using SMILES and Other Chemical Codes-Practical Solutions.
PMID:29186902
Computational approaches to chemical hazard assessment.
PMID:29101769
biochem4j: Integrated and extensible biochemical knowledge through graph databases.
PMID:28708831
Unique identifiers for small molecules enable rigorous labeling of their atoms.
PMID:28534867
The Drug Repurposing Hub: a next-generation drug library and information resource.
PMID:28388612
ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics.
PMID:28316655
Common cases of improper lipid annotation using high-resolution tandem mass spectrometry data and corresponding limitations in biological interpretation.
PMID:28263877
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data.
PMID:28158427
Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.
PMID:27929431
Glycosaminoglycanomics: where we are.
PMID:27900575
Experimental and Chemoinformatics Study of Tautomerism in a Database of Commercially Available Screening Samples.
PMID:27669079
Getting the most out of PubChem for virtual screening.
PMID:27454129
The Cambridge Structural Database.
PMID:27048719
Metabolomics by Gas Chromatography-Mass Spectrometry: Combined Targeted and Untargeted Profiling.
PMID:27038389
A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks.
PMID:26909353
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.
PMID:26481362
Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.
PMID:26457120
PubChem Substance and Compound databases.
PMID:26400175
The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets.
PMID:26155308
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.
PMID:26106450
A practical Java tool for small-molecule compound appraisal.
PMID:26082805
Many InChIs and quite some feat.
PMID:26081259
Quantum chemistry structures and properties of 134 kilo molecules.
PMID:25977779
CASMI: And the Winner is . .
PMID:24957999
On InChI and evaluating the quality of cross-reference links.
PMID:24742140
Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI.
PMID:22989151
The semantic architecture of the World-Wide Molecular Matrix (WWMM).
PMID:21999475
CMLLite: a design philosophy for CML.
PMID:21999395
Bioinformatics and systems biology of the lipidome.
PMID:21939287
Lipid classification, structures and tools.
PMID:21704189
Chemistry publication - making the revolution.
PMID:20142985
How large is the metabolome? A critical analysis of data exchange practices in chemistry.
PMID:19415114
Userscripts for the life sciences.
PMID:18154664
Correcting ligands, metabolites, and pathways.
PMID:17132165
Communication and re-use of chemical information in bioscience.
PMID:16026614