yusuke1997/dblp-id-title huggingface dataset:
HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model
Reply to "Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery"
Two years of explicit CiTO annotations
Molecular property prediction using pretrained-BERT and Bayesian active learning: a data-efficient approach to drug design
MDSuite: comprehensive post-processing tool for particle simulations
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy
New algorithms demonstrate untargeted detection of chemically meaningful changing units and formula assignment for HRMS data of polymeric mixtures in the open-source constellation web application
ChemSpectra: a web-based spectra editor for analytical data
SimBoost: a read-across approach for predicting drug-target binding affinities using gradient boosting machines
IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra
Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products
ChemicalToolBoX and its application on the study of the drug like and purchasable space
TRAVIS - a free analyzer and visualizer for Monte Carlo and molecular dynamics trajectories
QPHAR: quantitative pharmacophore activity relationship: method and validation
Random molecular substructures as fragment-type descriptors
Effect of missing data on multitask prediction methods
Recent and current developments in handling Markush structures from chemical patents
InChI version 1.06: now more than 99.99% reliable
Hamiltonian diversity: effectively measuring molecular diversity by shortest Hamiltonian circuits
XMetDB: an open access database for xenobiotic metabolism
Application of machine reading comprehension techniques for named entity recognition in materials science
The semantics of Chemical Markup Language (CML): dictionaries and conventions
UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers
DASPfind: new efficient method to predict drug-target interactions
Correction to: A new topological descriptor for water network structure
Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning
ChemTables: a dataset for semantic classification on tables in chemical patents
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model
SmartGraph: a network pharmacology investigation platform
The evolution of open science in cheminformatics: a journey from closed systems to collaborative innovation
MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning
Representation of Markush structures: from molecules toward patents
From eScience to iScience "I want Answers not Links" - new ways to search the Internet
Predicting RP-LC retention indices of structurally unknown chemicals from mass spectrometry data
Decrypting orphan GPCR drug discovery via multitask learning
Multi-fidelity graph neural networks for predicting toluene/water partition coefficients
Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
Context-dependent similarity searching for small molecular fragments
Molecular de-novo design through deep reinforcement learning
Molecule Set Comparator (MSC): a CDK-based open rich-client tool for molecule set similarity evaluations
BoBER: web interface to the base of bioisosterically exchangeable replacements
HybridGCN for protein solubility prediction with adaptive weighting of multiple features
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models
Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm
A 3D generation framework using diffusion model and reinforcement learning to generate multi-target compounds with desired properties
HYDEing the false positives - scoring for lead optimization
Toxicological knowledge discovery by mining emerging patterns from toxicity data
SimVec: predicting polypharmacy side effects for new drugs
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics
OrChem - An open source chemistry search engine for Oracle ®
Prediction of UGT-mediated phase II metabolism via ligand- and structure-based predictive models
HTA - An open-source software for assigning head and tail positions to monomer SMILES in polymerization reactions
A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
Molecular simulation grid
AI-powered prediction of critical properties and boiling points: a hybrid ensemble learning and QSPR approach
Atom-Atom-Path similarity and Sphere Exclusion clustering: tools for prioritizing fragment hits
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis
CPANNatNIC software for counter-propagation neural network to assist in read-across
Ligand based lead generation - considering chemical accessibility in rescaffolding approaches via BROOD
Open Babel: An open chemical toolbox
Predicting pKa values from EEM atomic charges
WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications
Assessing the calibration in toxicological in vitro models with conformal prediction
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome
Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons
Graph kernels for chemoinformatics - a critical discussion
SMPR: a structure-enhanced multimodal drug‒disease prediction model for drug repositioning and cold start
Activity-difference maps and consensus similarity measure characterize structure-activity relationships
Accurate structure-activity relationship prediction of antioxidant peptides using a multimodal deep learning framework
Programming languages in chemistry: a review of HTML5/JavaScript
CSearch: chemical space search via virtual synthesis and global optimization
bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming
Comparison and improvement of the predictability and interpretability with ensemble learning models in QSPR applications
Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier
rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization
Randomized SMILES strings improve the quality of molecular generative models
Automatic docking of a small number of ligands into a large number of binding sites
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2
HawkRank: a new scoring function for protein-protein docking based on weighted energy terms
FlaME: Flash Molecular Editor - a 2D structure input tool for the web
Chemical named entity recognition in the texts of scientific publications using the naïve Bayes classifier approach
Preliminary characterization of N-trimethylchitosan as a nanocarrier for malarie vaccine
Combination of fingerprints and MCS-based (inSARa) networks for Structure-Activity-Relationship analysis
A metadata-driven approach to data repository design
Parameterization to NDDO-based polarizable force field
Let's talk about rings
CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space
How frequently do clusters occur in hierarchical clustering analysis? A graph theoretical approach to studying ties in proximity
A computational model for predicting the transport of compounds by ABCC2
How to approach machine learning-based prediction of drug/compound-target interactions
IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data
Evaluating ligand docking methods for drugging protein-protein interfaces: insights from AlphaFold2 and molecular dynamics refinement
Flexible heuristic algorithm for automatic molecule fragmentation: application to the UNIFAC group contribution model
A new method for rapid comparison of protein binding pockets by capturing spatial distributions
Filtered circular fingerprints improve either prediction or runtime performance while retaining interpretability
Recognizing chemicals in patents: a comparative analysis
Bridging experiment and theory: a template for unifying NMR data and electronic structure calculations
Improving chemical disease relation extraction with rich features and weakly labeled data
InChI in the wild: An Assessment of InChIKey searching in Google
Prediction of compound-target interaction using several artificial intelligence algorithms and comparison with a consensus-based strategy
The pipelined metabolite identification based on MS fragmentation
JSME: a free molecule editor in JavaScript
Iterative machine learning-based chemical similarity search to identify novel chemical inhibitors
Learning important features from multi-view data to predict drug side effects
Predicting in silico electron ionization mass spectra using quantum chemistry
Ambiguity of non-systematic chemical identifiers within and between small-molecule databases
KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development
Bioisosteric similarity of drugs in virtual screening
Sort & Slice: a simple and superior alternative to hash-based folding for extended-connectivity fingerprints
Computational studies of flaviviruses: approaching to novel fusion inhibitors
NPCARE: database of natural products and fractional extracts for cancer regulation
Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization
Synergistic approach of structure-based and ligand-based drug design for the development of selective cannabinod receptor ligands
Ligand-side tautomer enumeration and scoring for structure-based drug-design
In silico polypharmacology: retrospective recognition vs. rational design
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder
Improved chemical text mining of patents using infinite dictionaries, translation and automatic spelling correction
Quantifying intrinsic chemical reactivity of molecular structural features for protein binding and reactive toxicity, using the MOSES chemoinformatics system
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules
vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available
Development of target focused library against drug target of P. falciparum using SVM and Molecular docking
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding
Semi-supervised prediction of protein fitness for data-driven protein engineering
Current aspects and future trends of computer-aided rescaffolding
Visualization of very large high-dimensional data sets as minimum spanning trees
kMoL: an open-source machine and federated learning library for drug discovery
Reply to the comment made by Šicho, Vorśilák and Svozil on 'The Power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability'
Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics
VGSC-DB: an online database of voltage-gated sodium channels
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond
GNINA 1.0: molecular docking with deep learning
InertDB as a generative AI-expanded resource of biologically inactive small molecules from PubChem
QligFEP: an automated workflow for small molecule free energy calculations in Q
A constructive approach for discovering new drug leads: Using a kernel methodology for the inverse-QSAR problem
Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets
Comment on "Advancing material property prediction: using physics-informed machine learning models for viscosity"
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata
QSAR modeling for In vitro assays: linking ToxCast™ database to the integrated modeling framework "OCHEM"
SAR and QSAR modeling of a large collection of LD50 rat acute oral toxicity data
Self organising hypothesis networks: a new approach for representing and structuring SAR knowledge
Prediction of the partition coefficient between air and body compartments from the chemical structure
Hydrogen placement in protein-ligand complexes under consideration of tautomerism
Blocking protein-protein interactions: the identification of repetitive turn structures as basis for inhibitor building blocks
InChI isotopologue and isotopomer specifications
Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models
Estimation of the biogas production rate, a chemometrical approach
A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example
Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors
STOUT: SMILES to IUPAC names using neural machine translation
QM quality atomic charges for proteins
PREDator - a new structure-based approach for cross-reactivity predictions
Paths to cheminformatics: Q&A with Nathaniel Charest
Optimizing drug-target interaction prediction based on random walk on heterogeneous networks
Deep learning integration of molecular and interactome data for protein-compound interaction prediction
Discriminating agonist and antagonist ligands of the nuclear receptors using 3D-pharmacophores
MetaboGNN: predicting liver metabolic stability with graph neural networks and cross-species data
More than a rigid framework: molecular design using secondary structure element information
Effects of using structured templates for recalling chemistry experiments
Targeting flexibility: a structure-based computational study revealing allosteric HIV-1 protease inhibitors
Analysis and visual summarization of molecular dynamics simulation
Computer-aided studies of molecular structure-comparison of measured and computed ECD spectra
Large-scale docking approaches to the kinome
Protecting your skin: a highly accurate LSTM network integrating conjoint features for predicting chemical-induced skin irritation
Assessing interaction recovery of predicted protein-ligand poses
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry
Comment on "The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability"
Applying the unified pH scale: absolute acidities in the gas phase and anchor points for eleven representative liquid media
Entropy gain due to water release upon ligand binding
CH5M3D: an HTML5 program for creating 3D molecular structures
Comparative analyses of structural features and scaffold diversity for purchasable compound libraries
The effect of noise on the predictive limit of QSAR models
Adoption of the Citation Typing Ontology by the Journal of Cheminformatics
JPlogP: an improved logP predictor trained using predicted data
LICSS - a chemical spreadsheet in microsoft excel
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions
Improving VAE based molecular representations for compound property prediction
HSQC spectral based similarity matching of compounds using nearest neighbours and a fast discrete genetic algorithm
Discovering HDAC class II selective inhibitors by multidisciplinary approach
Building shape-focused pharmacophore models for effective docking screening
Rapid binding site analysis by means of structural interaction fingerprint patterns - an implication to GPCR-targeted CADD
Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity
Compressed graph representation for scalable molecular graph generation
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images
SkinSensDB: a curated database for skin sensitization assays
A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding
Advanced SPARQL querying in small molecule databases
Multi-task learning with a natural metric for quantitative structure activity relationship learning
A multiple classifier system identifies novel cannabinoid CB2 receptor ligands
Blood-brain barrier penetration prediction enhanced by uncertainty estimation
CardioTox net: a robust predictor for hERG channel blockade based on deep learning meta-feature ensembles
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank
Small molecule autoencoders: architecture engineering to optimize latent space utility and sustainability
IntelliPatent: a web-based intelligent system for fast chemical patent claim drafting
Evaluation of a Bayesian inference network for ligand-based virtual screening
Performance of dispersion-corrected density functional theory for thermochemistry and non-covalent interactions
A new chemoinformatics approach with improved strategies for effective predictions of potential drugs
ReactionT5: a pre-trained transformer model for accurate chemical reaction prediction with limited data
Thermodynamic models and factual data banks - ideal tools for the development of chemical processes
Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds
Targeting protein dynamics in drug design
How can SHAP values help to shape metabolic stability of chemical compounds?
The assessment of computationally derived protein ensembles in protein-ligand docking
RetroRanker: leveraging reaction changes to improve retrosynthesis prediction through re-ranking
A new workflow for the effective curation of membrane permeability data from open ADME information
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
Predicting protein-protein interactions with DrugScore PPI : fully-flexible docking, scoring, and in silico alanine-scanning
A theoretical investigation of microhydration of amino acids
ProLIF: a library to encode molecular interactions as fingerprints
Semantic physical science
Statistical principle-based approach for gene and protein related object recognition
Geometric deep learning for molecular property predictions with chemical accuracy across chemical space
MolData, a molecular benchmark for disease and target based machine learning
Efficient ring perception for the Chemistry Development Kit
Commentary: the first twelve years of the Journal of chemoinformatics
Fingerprint-based detection of acute aquatic toxicity
DECIMER - hand-drawn molecule images dataset
Voting-based consensus clustering for combining multiple clusterings of chemical structures
ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics
Indigo: universal cheminformatics API
TB mobile: a mobile app for anti-tuberculosis molecules with known targets
A visual approach for analysis and inference of molecular activity spaces
Efficient iterative virtual screening with Apache Spark and conformal prediction
Kernel learning for ligand-based virtual screening: discovery of a new PPARγ agonist
Ionization efficiency prediction of electrospray ionization mass spectrometry analytes based on molecular fingerprints and cumulative neutral losses
ProfhEX: AI-based platform for small molecules liability profiling
Modifications to glucose-6-phosphate dehydrogenase for industrial applications: predictions and tests
Review of "Data Analysis with Open Source Tools" by Philipp K Janert
PyL3dMD: Python LAMMPS 3D molecular descriptors package
On the validity versus utility of activity landscapes: are all activity cliffs statistically significant?
A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD
Predicting liver cytosol stability of small molecules
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
PubChem3D: Similar conformers
Evaluation of chirality descriptors derived from SMILES heteroencoders
DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature
HIM-herbal ingredients in-vivo metabolism database
Correction to: Designing optimized drug candidates with Generative Adversarial Network
Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes
tt DiffER: categorical diffusion ensembles for single-step chemical retrosynthesis
Chemistry publication - making the revolution
An ensemble model of QSAR tools for regulatory risk assessment
Application of a chemical reactivity database to predict toxicity for reactive mechanisms
DockStream: a docking wrapper to enhance de novo molecular design
SMARTS-RX: a SMARTS-based representation of chemical functions for reactivity analysis
CyBy 2 : a strongly typed, purely functional framework for chemical data management
MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry
"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool
QSAR DataBank repository: open and linked qualitative and quantitative structure-activity relationship models
Mining public-source databases for structure-activity relationships
Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization
Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach
Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
Molecular representations in AI-driven drug discovery: a review and practical guide
Improving chemical reaction yield prediction using pre-trained graph neural networks
A comprehensive analysis of the history of DFT based on the bibliometric method RPYS
Transformer-based molecular optimization beyond matched molecular pairs
chemfp - fast and portable fingerprint formats and tools
Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction
Limits to molecular matched-pair analysis: the experimental uncertainty case
Accuracy enhancement in the estimation of molecular hydration free energies by implementing the intramolecular hydrogen bond effects
TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson
The integration of Open3DTOOLS into the RDKit and KNIME
5th German Conference on Chemoinformatics: 23. CIC-Workshop. November 8-10, 2009, Goslar, Germany
GNINA 1.3: the next increment in molecular docking with deep learning
Addressing standardization and semantics in an electronic lab notebook for multidisciplinary use: LabIMotion
Comparing structural fingerprints using a literature-based similarity benchmark
Predicting inhibitors of OATP1B1 via heterogeneous OATP-ligand interaction graph neural network (HOLIgraph)
Drug Repositioning: A Machine-Learning Approach through Data Integration
SpeckTackle: JavaScript charts for spectroscopy
Predicting the protein targets for athletic performance-enhancing substances
School of cheminformatics in Latin America