yusuke1997/dblp-id-title huggingface dataset:
Ketcher: web-based chemical structure editor
EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation
Compound optimization through data set-dependent chemical transformations
PubChem: atom environments for molecule standardization
ChemSAR: an online pipelining platform for molecular SAR modeling
Confidence bands and hypothesis tests for hit enrichment curves
Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents
Towards the prediction of drug solubility in binary solvent mixtures at various temperatures using machine learning
Cobdock: an accurate and practical machine learning-based consensus blind docking method
Comparing manual and automated extraction of chemical entities from documents
Cross-validation pitfalls when selecting and assessing regression and classification models
Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature
Adaptive matrix metrics for molecular descriptor assessment in QSPR classification
jsMolEditor: an open source molecule editor for the next generation web
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data
Predicting protein network topology clusters from chemical structure using deep learning
Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph
How to build machine learning models able to extrapolate from standard to modified peptides
Muse+TriposScore: a ligand-based de novo design approach
Pt(II) and Pt(IV) complexes with large hydrophobic ligands: a study of new potential cytostatics
Infrared spectrum analysis of organic molecules with neural networks using standard reference data sets in combination with real-world data
From molecules to data: the emerging impact of chemoinformatics in chemistry
Template-based combinatorial enumeration of virtual compound libraries for lipids
A new software for fragment-based QSAR and its applications
CSgator: an integrated web platform for compound set analysis
Structure-based identification of dual ligands at the A 2A R and PDE10A with anti-proliferative effects in lung cancer cell-lines
What makes a reaction network "chemical"?
A new topological descriptor for water network structure
Semantic science and its communication - a personal view
Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)
Visualization and virtual screening in molecular property spaces
Predicting the critical micelle concentration of binary surfactant mixtures using machine learning
Representation of chemistry transport models simulations using knowledge graphs
Complementary PLS and KNN algorithms for improved 3D-QSDAR consensus modeling of AhR binding
C2PO: an ML-powered optimizer of the membrane permeability of cyclic peptides through chemical modification
Deep learning molecular interaction motifs from receptor structures alone
Simulation of the influence of oxygen on the chemical stage of radiobiological mechanism using Petri nets
Analysis of naphthoquinone derivatives as topoisomerase I inhibitors using fragment based QSAR
Learning motif features and topological structure of molecules for metabolic pathway prediction
A quantum chemical dataset of interacting molecular pairs for chemical reaction studies
Improving the accuracy of prediction models for small datasets of Cytochrome P450 inhibition with deep learning
A systematic review of deep learning chemical language models in recent era
Looking over the rim: algorithms for cheminformatics from computer scientists
Retrosynthetic crosstalk between single-step reaction and multi-step planning
Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets
Visualising lead optimisation series using reduced graphs
ParaDockS - an open source framework for molecular docking
Progress on an open source computer-assisted structure elucidation suite (SENECA)
Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics
The influence of hashed fingerprints density on the machine learning methods performance
Postprocessing of molecular docking poses using binding free energy calculations
Confab - generation of diverse low energy conformers
AiGPro: a multi-tasks model for profiling of GPCRs for agonist and antagonist
Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies
Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data
Improving chemical entity recognition through h-index based semantic similarity
HD_BPMDS: a curated binary pattern multitarget dataset of Huntington's disease-targeting agents
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
Bringing the MMFF force field to the RDKit: implementation and validation
Finding the K best synthesis plans
Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action
Generative model based on junction tree variational autoencoder for HOMO value prediction and molecular optimization
COVER: conformational oversampling as data augmentation for molecules
Optimal assignment methods for ligand-based virtual screening
Benchmarking ML in ADMET predictions: the practical impact of feature representations in ligand-based models
Correction: QuanDB: a quantum chemical property database towards enhancing 3D molecular representation learning
An in silico MS/MS library for automatic annotation of novel FAHFA lipids
MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle
One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening
Biomedical data analyses facilitated by open cheminformatics workflows
Cheminformatics Microservice: unifying access to open cheminformatics toolkits
Kernel-based estimation of the applicability domain of QSAR models
Fast, efficient fragment-based coordinate generation for Open Babel
Solvent-screening and co-crystal screening for drug development with COSMO-RS
Fast rule-based bioactivity prediction using associative classification mining
Erratum to: Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes
Binding mode information improves fragment docking
A novel descriptor based on atom-pair properties
Large scale study of multiple-molecule queries
POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor
GESim: ultrafast graph-based molecular similarity calculation via von Neumann graph entropy
Probing the impact of protein and ligand preparation procedures on chemotype enrichment in structure-based virtual screening using DEKOIS 2.0 benchmark sets
FPocketWeb: protein pocket hunting in a web browser
MetaRF: attention-based random forest for reaction yield prediction with a few trails
Full "Laplacianised" posterior naive Bayesian algorithm
DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state
Systems biology approaches for advancing the discovery of effective drug combinations
Molecular modeling of lipid drug formulations
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes
Scoria: a Python module for manipulating 3D molecular data
Combining graph neural networks and transformers for few-shot nuclear receptor binding activity prediction
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision
A generalizable definition of chemical similarity for read-across
Pairwise structural comparison of tiagabine analogs gives new insights into their protein binding modes
Mind your prevalence!
Reproducibility in cheminformatics and computational chemistry research: certainly we can do better than this
Maximum-score diversity selection for early drug discovery
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 1: Theory and characteristics †
The CHEMDNER corpus of chemicals and drugs and its annotation principles
The C++ programming language in cheminformatics and computational chemistry
Distance plus attention for binding affinity prediction
PubChem structure-activity relationship (SAR) clusters
SuperMetal: a generative AI framework for rapid and precise metal ion location prediction in proteins
BCL: : Conf: small molecule conformational sampling using a knowledge based rotamer library
ChemProspector and generic structures: advanced mining and searching of chemical content
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques
Mapping and classifying molecules from a high-throughput structural database
Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis
Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds
Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals
3D pharmacophore alignments: does improved geometric accuracy affect virtual screening performance?
Efficient enumeration of monocyclic chemical graphs with given path frequencies
How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver
Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library
European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials
rBAN: retro-biosynthetic analysis of nonribosomal peptides
Correction: Reconstruction of lossless molecular representations from fingerprints
Random forests for feature selection in QSPR Models - an application for predicting standard enthalpy of formation of hydrocarbons
Applied and implied semantics in crystallographic publishing
Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?
LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions
osFP: a web server for predicting the oligomeric states of fluorescent proteins
The MoSGrid - e-science gateway: molecular simulations in a distributed computing environment
CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling
LOGICS: Learning optimal generative distribution for designing de novo chemical structures
hERGAT: predicting hERG blockers using graph attention mechanism through atom- and molecule-level interaction analyses
Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning
Computational mass spectrometry for small molecules
Cheminformatics Microservice V3: a web portal for chemical structure manipulation and analysis
QSAR of anti-inflammatory drugs
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes
Enhancing molecular property prediction with auxiliary learning and task-specific adaptation
Charged aerosol detector response modeling for fatty acids based on experimental settings and molecular features: a machine learning approach
Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction
Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data
Design, implementation, and operation of a rapid, robust named entity recognition web service
The diatomic molecular spectroscopy database
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm
Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets
Avogadro: An advanced semantic chemical editor, visualization, and analysis platform
QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction
MyChemise: a 2D drawing software that uses morphing for visualisation purposes
Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses
CHEMDNER system with mixed conditional random fields and multi-scale word clustering
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES
MATEO: intermolecular α-amidoalkylation theoretical enantioselectivity optimization. Online tool for selection and design of chiral catalysts and products
Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features
The first South Korean data challenge for drug discovery using human and mouse liver microsomal stability data
What's new in KNIME?
Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening
Systemic evolutionary chemical space exploration for drug discovery
Nonpher: computational method for design of hard-to-synthesize structures
Journal of Cheminformatics, ORCID, and GitHub
Searching chemical databases in the pre-history of cheminformatics
A unified approach to the applicability domain problem of QSAR models
Explainable uncertainty quantifications for deep learning-based molecular property prediction
Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition
Deep generative model for drug design from protein target sequence
Learning cheminformatics
Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians
Application of deep metric learning to molecular graph similarity
LeadMine: a grammar and dictionary driven approach to entity recognition
Enalos KNIME nodes: exploring environmental durability, ageing resistance and corrosion inhibition
tmChem: a high performance approach for chemical named entity recognition and normalization
A computational workflow for analysis of missense mutations in precision oncology
Cheminformatics-based enumeration and analysis of large libraries of macrolide scaffolds
KMR: knowledge-oriented medicine representation learning for drug-drug interaction and similarity computation
Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines
NMR shift prediction from small data quantities
patRoon: open source software platform for environmental mass spectrometry based non-target screening
A framework and workflow system for virtual screening and molecular docking
Stability of single and double layer fibrillar amyloid-β oligomers
Generation of structure-based pharmacophores using energetic analysis - application on fragment docking
Quantitative prediction of selectivity between the A 1 and A 2A adenosine receptors
An automatic system for the simultaneous translation of lectures
Scaffold hunter: visual analysis of biological activity data
Art driven by visual representations of chemical space
Can quantum-chemical NMR chemical shifts be used as criterion for force-field development
From Big Data to Artificial Intelligence: chemoinformatics meets new challenges
In silico prediction of UGT-mediated metabolism in drug-like molecules via graph neural network
Ligand cluster-based protein network and ePlatton, a multi-target ligand finder
Classification of substances by health hazard using deep neural networks and molecular electron densities
A large scale classification of molecular fingerprints for the chemical space representation and SAR analysis
Theoretical NMR correlations based Structure Discussion
Use of DEKOIS 2.0 to gain insights for virtual screening
Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach
Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry
Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration
SAR Analyzer: a tool for interactive SAR data visualization and navigation
jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints
Making the most of approximate maximum common substructure search
AttenhERG: a reliable and interpretable graph neural network framework for predicting hERG channel blockers
PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules
International chemical identifier for chemical reactions
Ion permeation through neuronal nAChR ion channel
Evolution of DFT studies in view of a scientometric perspective
A confidence predictor for logD using conformal regression and a support-vector machine
Investigation of chemical structure recognition by encoder-decoder models in learning progress
DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning
The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration
The development of models to predict melting and pyrolysis point data associated with several hundred thousand compounds mined from PATENTS
PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction
Multi-objective de novo drug design with conditional graph generative model
Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies
PharmDock: a pharmacophore-based docking program
Craig plot 2.0: an interactive navigation in the substituent bioisosteric space
PubChem chemical structure standardization
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification
Virtual screening of bioassay data
Crossover operators for molecular graphs with an application to virtual drug screening
Reverse engineering molecules from fingerprints through deterministic enumeration and generative models
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19
Chemical entity extraction using CRF and an ensemble of extractors
Probing the chemical-biological relationship space with the Drug Target Explorer
Quantitative structure-activity relationships of chemical bioactivity toward proteins associated with molecular initiating events of organ-specific toxicity
RanDepict: Random chemical structure depiction generator
Assessment of a probabilistic framework for combining structure- and ligand-based virtual screening
Bayesian optimization for conformer generation
Charge-related topological index - various chemoinformatics applications
Theoretical studies on cycloaddition reactions
CRFVoter: gene and protein related object recognition using a conglomerate of CRF-based tools
QSPR designer - a program to design and evaluate QSPR models. Case study on pK a prediction
PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment
Interoperable chemical structure search service
Synergy Maps: exploring compound combinations using network-based visualization
Semi-empirical derived descriptors for the modelling of properties of N-containing heterocycles
Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints
PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow
OSCAR4: a flexible architecture for chemical text-mining
Phototoxicity - from molecular descriptors to classification models
A fast topological analysis algorithm for large-scale similarity evaluations of ligands and binding pockets
De novo design of selective compounds: a fragment-based pipeline applied to the β2 adrenergic receptor
Physicochemical modelling of the retention mechanism of temperature-responsive polymeric columns for HPLC through machine learning algorithms
An automated framework for NMR chemical shift calculations of small organic molecules
The influence of training actives/inactives ratio on machine learning performance
Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening
Visualization of chemical space for medicinal chemists
Interaction studies of Alzheimer's Cathepsin B protein with inhibitors in presence and absence of water
ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files
Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability
DrugTax: package for drug taxonomy identification and explainable feature extraction
Sachem: a chemical cartridge for high-performance substructure search
Evaluation of molecular model-based discovery of ecto-5'-nucleotidase inhibitors on the basis of X-ray structures
Target prediction by cascaded self-organizing maps for ligand de-orphaning and side-effect investigation
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach
Development of target-biased scoring functions for protein-ligand docking
Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models
Fast automated placement of polar hydrogen atoms in protein-ligand complexes
QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool
Generative design of compounds with desired potency from target protein sequences using a multimodal biochemical language model
ReMODE: a deep learning-based web server for target-specific drug design
Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT
Evaluating the generalizability of graph neural networks for predicting collision cross section
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling
Fishing out the signal in polypharmacological high-throughput screening data using novel navigator cheminformatics software
Semantic Web integration of Cheminformatics resources with the SADI framework
On the validity of popular assumptions in computational drug design
3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal
Automated annotation of chemical names in the literature with tunable accuracy
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations
CHEMDNER: The drugs and chemical names extraction challenge
Hybrid semantic recommender system for chemical compounds in large-scale datasets
Computational chemistry in pharmaceutical research - where do we stand after 25 years?
Adventures in public data
Computer-guided discovery of epigenetics drugs: molecular modeling and identification of inhibitors of DNMT1
Supervised extensions of chemography approaches: case studies of chemical liabilities assessment
Force field-inspired molecular representation learning for property prediction
MER: a shell script and annotation server for minimal named entity recognition and linking
Reaction rebalancing: a novel approach to curating reaction databases
In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion
MOLE 2.0: advanced approach for analysis of biomacromolecular channels