yusuke1997/dblp-id-title huggingface dataset:
Are new ideas harder to find? A note on incremental research and Journal of Cheminformatics' Scientific Contribution Statement
Advancing material property prediction: using physics-informed machine learning models for viscosity
Fragment-based identification of multi-target ligands by self-organizing map alignment
Inferring potential small molecule-miRNA association based on triple layer heterogeneous network
DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning
A molecular fragment cheminformatics roadmap for mesoscopic simulation
Druggable chemical space and enumerative combinatorics
Prediction of small-molecule compound solubility in organic solvents by machine learning algorithms
A transformer based generative chemical language AI model for structural elucidation of organic compounds
ELNdataBridge: facilitating data exchange and collaboration by linking Electronic Lab Notebooks via API
Challenges in agrochemicals design
Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization
HobPre: accurate prediction of human oral bioavailability for small molecules
Improving the performance of models for one-step retrosynthesis through re-ranking
Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data
Software platform virtualization in chemistry research and university teaching
Structured chemical class definitions and automated matching for chemical ontology evolution
11th German Conference on Chemoinformatics (GCC 2015) - Fulda, Germany. 8-10 November 2015
Design of multi-target activity landscapes that capture hierarchical activity cliff distributions
Uncertainty-aware prediction of chemical reaction yields with graph neural networks
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study
Badapple: promiscuity patterns from noisy evidence
TraceMetrix: a traceable metabolomics interactive analysis platform
Towards automated metabolome assembly: application of text mining to correlate small molecules, targets and tissues
Computational metabolomics - a field at the boundaries of cheminformatics and bioinformatics
Prediction of highly-connected 'hub'-proteins in protein interaction networks using QSAR
LEADD: Lamarckian evolutionary algorithm for de novo drug design
Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance
The membrane bound aromatic p-hydroxybenzoic acid oligoprenyltransferase (UbiA) - how iterative improvements lead to a realistic structure that offers new insights into functional aspects of prenyl transferases and terpene synthases
DeepTGIN: a novel hybrid multimodal approach using transformers and graph isomorphism networks for protein-ligand binding affinity prediction
A numerical compass for experiment design in chemical kinetics and molecular property estimation
ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database
Development of cannabinoid receptor (CB 2 R) ligands for application in PET studies - where to attach the radiolabel?
Leveraging 3D chemical similarity, target and phenotypic data in the identification of drug-protein and drug-adverse effect associations
In silico target prediction: identification of on- and off-targets for crop protection agents
A CRF-based system for recognizing chemical entity mentions (CEMs) in biomedical literature
Introducing fuzziness into maximum common substructures for meaningful cluster characterisation
How often do follow-on activities occur - trends seen in a patent database for GPCRs
PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications
Identification of hot-spot regions of N-type Ca 2+ channel receptor by homology modeling and molecular dynamics study, for structure-based blocker design
Improving drug repositioning with negative data labeling using large language models
On InChI and evaluating the quality of cross-reference links
Conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator
Systematic search for pairwise dependencies of torsion angles
Pharmacological affinity fingerprints derived from bioactivity data for the identification of designer drugs
Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures
Cross-validation is dead. Long live cross-validation! Model validation based on resampling
Efficient learning of non-autoregressive graph variational autoencoders for molecular graph generation
Naturally-meaningful and efficient descriptors: machine learning of material properties based on robust one-shot ab initio descriptors
Where are the boundaries? Automated pocket detection for druggability studies
MONA - Interactive manipulation of molecule collections
Anticipating protein evolution with successor sequence predictor
Collaborative development of predictive toxicology applications
Application of spectrophores™ to map vendor chemical space using self-organising maps
DecoyFinder, a tool for finding decoy molecules
Machine learning-driven generation and screening of potential ionic liquids for cellulose dissolution
Structure-based, deep-learning models for protein-ligand binding affinity prediction
Consensus holistic virtual screening for drug discovery: a novel machine learning model approach
Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets
DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions
Reliable estimation of externally validated prediction errors for QSAR models
Annotating targets with pathways: extending approaches to mode of action analysis
High-quality and universal empirical atomic charges for chemoinformatics applications
3D-QSAR reloaded: Open3DALIGN meets COSMOsar3D
Learning antibacterial activity against S. Aureus on the Chimiothèque Nationale dataset
Expanding the fragrance chemical space for virtual screening
A rule-based algorithm for automatic bond type perception
Predicting cytotoxicity from heterogeneous data sources with Bayesian learning
A combined combinatorial and pKa-based approach to ligand protonation states
Activity cliff-aware reinforcement learning for de novo drug design
Cheminformatics and computational chemistry in lead optimisation
Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery
chemf: A purely functional chemistry toolkit
IterTunnel; a method for predicting and evaluating ligand EgressTunnels in proteins with buried active sites
A comparative study of in silico prediction of pK a
Fragmentation trees reloaded
Non-continuum solvation using the EC-RISM method applied to predict tautomer ratios, pK a and enantiomeric excess of alkylation reactions
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL
"We were here before the Web and hype...": a brief history of and tribute to the Computational Chemistry List
Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices
Ionotropic GABA receptors: modelling and design of selective ligands
PoseView - molecular interaction patterns at a glance
The importance of template choice in homology modeling. A 5-HT 6 R case study
Text-based similarity searching for hit- and lead-candidate identification
Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data
Correction: Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling
FragVLib a free database mining software for generating "Fragment-based Virtual Library" using pocket similarity search of ligand-receptor complexes
Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent
A unified approach to inferring chemical compounds with the desired aqueous solubility
FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data
Deepmol: an automated machine and deep learning framework for computational chemistry
Elucidating protein-protein interactions using the HYDE scoring function
Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening
Statistical-based database fingerprint: chemical space dependent representation of compound databases
Human-in-the-loop active learning for goal-oriented molecule generation
Enhanced Thompson sampling by roulette wheel selection for screening ultralarge combinatorial libraries
DFFNDDS: prediction of synergistic drug combinations with dual feature fusion networks
Machine intelligence-driven framework for optimized hit selection in virtual screening
Life beyond the Tanimoto coefficient: similarity measures for interaction fingerprints
COCONUT online: Collection of Open Natural Products database
A document processing pipeline for annotating chemical entities in scientific documents
Standards-based curation of a decade-old digital repository dataset of molecular information
Predicting drug polypharmacology using a novel surface property similarity-based approach
Docking based 3D-QSAR studies applied at the BRAF inhibitors to understand the binding mechanism
SMILES all around: structure to SMILES conversion for transition metal complexes
Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods
HERGAI: an artificial intelligence tool for structure-based prediction of hERG inhibitors
Efficient mining of protein kinase structural data
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining (Correction)
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles
Surflex-QMOD: physically meaningful QSAR
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map
Visualizing chemical space networks with RDKit and NetworkX
Making SharePoint ® Chemically Aware™
Improved estimation of intrinsic solubility of drug-like molecules through multi-task graph transformer
Molecular modelling studies of synthesized pentacyclo-undecane peptides as potential HIV-1 wild type C-SA protease inhibitors
MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data
Homology modelling of metabotropic glutamate receptor 2
What is the role of cheminformatics in a pandemic?
Interpreting vibrational circular dichroism spectra: the Cai•factor for absolute configuration with confidence
Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions
The CompTox Chemistry Dashboard: a community data resource for environmental chemistry
Applicability domain for classification problems
Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR
Making people's lives easier, better and more beautiful - and how computer-aided materials design may help
Solvent flashcards: a visualisation tool for sustainable chemistry
New developments on the cheminformatics open workflow environment CDK-Taverna
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges
Practical guidelines for the use of gradient boosting for molecular property prediction
Software solutions for evaluation and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI) data: a short overview
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set
Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning
Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases
An automated framework for QSAR model building
Generative artificial intelligence based models optimization towards molecule design enhancement
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis
Machine learning approaches to optimize small-molecule inhibitors for RNA targeting
Diversity oriented Deep Reinforcement Learning for targeted molecule generation
ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding
GPCR-A17 MAAP: mapping modulators, agonists, and antagonists to predict the next bioactive target
kGCN: a graph-based deep learning framework for chemical structures
Chemoinformatics-based enumeration of chemical libraries: a tutorial
2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope
Substructure-based neural machine translation for retrosynthetic prediction
Predictive modeling of visible-light azo-photoswitches' properties using structural features
Exploring the GDB-13 chemical space using deep generative models
In-silico Predictive Mutagenicity Model Generation Using Supervised Learning Approaches
A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases
Multi-modal contrastive drug synergy prediction model guided by single modality
A reliable computational workflow for the selection of optimal screening libraries
QSAR-Co-X: an open source toolkit for multitarget QSAR modelling
A note on utilising binary features as ligand descriptors
MOGADOC: a database with 3D-structures
Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model
Box embeddings for extending ontologies: a data-driven and interpretable approach
Structure-activity relationship-based chemical classification of highly imbalanced Tox21 datasets
"DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases
Guiding protein-ligand docking with different experimental NMR-data
pharmACOphore: multiple flexible ligand alignment based on ant colony optimization
Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2
Rubabel: Wrapping OpenBabel with Ruby
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods
RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions
Using GANs with adaptive training data to search for new molecules
Visual analytics in cheminformatics: user-supervised descriptor selection for QSAR methods
Aligning chemical structure diagrams with local search
OPERA models for predicting physicochemical properties and environmental fate endpoints
Three pillars for ensuring public access and integrity of chemical databases powering cheminformatics
Modular Chemical Descriptor Language (MCDL): Stereochemical modules
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES
Evaluation of deep and shallow learning methods in chemogenomics for the prediction of drugs specificity
Molecular simulations of peptides and proteins with Molecular Fragment Dynamics (MFD)
Force-field-based minimizations of protein-ligand complexes in the blink of an eye
Using beta binomials to estimate classification uncertainty for ensemble models
Harnessing Shannon entropy-based descriptors in machine learning models to enhance the prediction accuracy of molecular properties
Blind trials of computer-assisted structure elucidation software
Embedded infrastructure for primary data in chemistry
The FPS fingerprint format and chemfp toolkit
Correction: MOFGalaxyNet: a social network analysis for predicting guest accessibility in metal-organic frameworks utilizing graph convolutional networks
FMCS: a novel algorithm for the multiple MCS problem
Context-dependent similarity analysis of analogue series for structure-activity relationship transfer based on a concept from natural language processing
Predicting the protein localization sites using artificial neural networks
Protein modeling and molecular dynamic studies of two new surfactant proteins
RANdom SAmple Consensus (RANSAC) algorithm for material-informatics: application to photovoltaic solar cells
Theoretical and experimental study of the pH-dependent interaction of amino acids and MFI-type zeolite
Improving chemical similarity ensemble approach in target prediction
Towards understanding the chemical environment effect on gold-containing clusters
Ami - The chemist's amanuensis
InChI: a user's perspective
HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors
ChEBI: a chemistry ontology and database
Interpreting linear support vector machine models with heat map molecule coloring
Computational evaluation of the η6-arene during the ATH of imines on Noyori's RuII catalyst
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks
COMA: efficient structure-constrained molecular generation using contractive and margin losses
Hand in the snow
MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model
Correction : Random-forest model for drug-target interaction prediction via Kullback-Leibler divergence
LinChemIn: SynGraph - a data model and a toolkit to analyze and compare synthetic routes
Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability
Multi-channel PINN: investigating scalable and transferable neural networks for drug discovery
Cache: Utilizing ultra-large library screening in Rosetta to identify novel binders of the WD-repeat domain of Leucine-Rich Repeat Kinase 2
Dataset overlap density analysis
A graph-based approach to construct target-focused libraries for virtual screening
KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study
Empirical charges for chemoinformatics applications
Discovery of novel α-amylase inhibitors using structure-based drug design
Mining chemical information from open patents
DPRESS: Localizing estimates of predictive uncertainty
Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation
Defining a novel k-nearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions
Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants
RepTB: a gene ontology based drug repurposing approach for tuberculosis
Accurate and efficient target prediction using a potency-sensitive influence-relevance voter
Machine learning for identification of silylated derivatives from mass spectra
BioisoIdentifier: an online free tool to investigate local structural replacements from PDB
Generating diversity and securing completeness in algorithmic retrosynthesis
RRegrs: an R package for computer-aided model selection with multiple regression models
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids
PubChem3D: Conformer generation
chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery
CalVSP: a program for analyzing the molecular surface areas, volumes, and polar surface areas
G.A.M.E.: GPU-accelerated mixture elucidator
Predictive modeling of biodegradation pathways using transformer architectures
Too many tags spoil the metadata: investigating the knowledge management of scientific research with semantic web technologies
CADDSuite - a workflow-enabled suite of open-source tools for drug discovery
PubChem3D: conformer ensemble accuracy
Towards interoperable and reproducible QSAR analyses: Exchange of datasets
Correction to: Pharmacological affinity fingerprints derived from bioactivity data for the identification of designer drugs
Reliable and accurate prediction of basic pK a values in nitrogen compounds: the pK a shift in supramolecular systems as a case study
CLAIRE: a contrastive learning-based predictor for EC number of chemical reactions
A ranking method for the concurrent learning of compounds with various activity profiles
Exploring and cataloguing the substrate space of prenyltransferases: automatic generation of SMARTS
Molpher: a software framework for systematic chemical space exploration
AdapTor: Adaptive Topological Regression for quantitative structure-activity relationship modeling
SGEDiff: a subgraph-enriched diffusion model for structure-based 3D molecular generation
Review on natural products databases: where to find data in 2020
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information
AI/ML methodologies and the future-will they be successful in designing the next generation of new chemical entities?
Deep learning of multimodal networks with topological regularization for drug repositioning
CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution
PIKAChU: a Python-based informatics kit for analysing chemical units
Development of a pharmacorphore model for pharmacological chaperones targeting mutant trafficking-deficient CNG channels
Pharmacophore annotation using extended Hückel theory
Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods
Chemoinformatics in drug development
Chemoinformatics and structural bioinformatics in OCaml
Multilevel Parallelization of AutoDock 4.2
Shape: automatic conformation prediction of carbohydrates using a genetic algorithm
A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood
An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites
Reliable estimation of prediction errors for QSAR models under model uncertainty using double cross-validation
CReM: chemically reasonable mutations framework for structure generation
Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization
Quantifying model errors using similarity to training data
ChemDIS: a chemical-disease inference system based on chemical-protein interactions
Multi-parameter scoring functions for ligand- and structure-based de novo design
Adaptation of formal concept analysis for the systematic exploration of structure-activity and structure-selectivity relationships
Maximizing gain in high-throughput screening using conformal prediction
Dataset's chemical diversity limits the generalizability of machine learning predictions
A de novo molecular generation method using latent vector based generative adversarial network
Identification of SUMO activating enzyme 1 inhibitors utilizing virtual screening approach
How evaluation choices distort the outcome of generative drug discovery
Sodium dependent glucose transporter (SGLT) 1 / 2 - elucidating inhibitor SAR and selectivity using homology modelling and 3D QSAR studies
MAIP: a web service for predicting blood-stage malaria inhibitors
Searching substructures in fragment spaces
Impact of binding site waters on inhibitor design: contemplating a novel inverse binding mode of indirubin derivatives in DYRK kinases
OGER++: hybrid multi-type entity recognition
Using graph-based consensus clustering for combining K-means clustering of heterogeneous chemical structures
KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking