yusuke1997/dblp-id-title huggingface dataset:
Correction: StreaMD: the toolkit for high-throughput molecular dynamics simulations
A multi-view feature representation for predicting drugs combination synergy based on ensemble and multi-task attention models
Validated scoring of halogen bonding in molecular design
Assessment of a variety of dispersion-corrected density functional theory calculations used in molecular crystal structure prediction
Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag
SiteHopper - a unique tool for binding site comparison
Searching for tunnels of proteins - comparison of approaches and available software tools
xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides
The status of the InChI project and the InChI trust
Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates
New insights on the interface between metal oxide and biosystem
LigpKa - a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations
Tora3D: an autoregressive torsion angle prediction model for molecular 3D conformation generation
DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data
A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening
The rcdk and cluster R packages applied to drug candidate selection
DeepAR: a novel deep learning-based hybrid framework for the interpretable prediction of androgen receptor antagonists
Mapping the 3D structures of small molecule binding sites
Asymmetric transfer hydrogenation of imines and ketones using chiral Ru(II)Cl(η 6 -p-cymene)[(S, S)-N-TsDPEN] catalyst: a computational study
HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines
Multiobjective de novo drug design with recurrent neural networks and nondominated sorting
Computational modeling, docking and molecular dynamics of the transcriptional activator ComA bound to a newly-identified functional DNA binding site
Confab - Systematic generation of diverse low-energy conformers
Explaining compound activity predictions with a substructure-aware loss for graph neural networks
A multitask GNN-based interpretable model for discovery of selective JAK inhibitors
Milestones in cheminformatics
Correction to: The chemfp project
ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics
CMLLite: a design philosophy for CML
Web-based 3D-visualization of the DrugBank chemical space
Database fingerprint (DFP): an approach to represent molecular databases
A review of optical chemical structure recognition tools
Neural machine translation of chemical nomenclature between English and Chinese
Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules
Taking the PubChem web sketcher to the next level
A document classifier for medicinal chemistry publications trained on the ChEMBL corpus
Implementation of a soft grading system for chemistry in a Moodle plugin: reaction handling
Efficiency of different measures for defining the applicability domain of classification models
QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations
Atomistic details of the phosphodiester cleavage of ribonuclease H
Random-forest model for drug-target interaction prediction via Kullbeck-Leibler divergence
Consistency of systematic chemical identifiers within and between small-molecule databases
CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures
UniChem: a unified chemical structure cross-referencing and identifier tracking system
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop
Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision
Beyond performance: how design choices shape chemical language models
Ualign: pushing the limit of template-free retrosynthesis prediction with unsupervised SMILES alignment
When drug discovery meets web search: Learning to Rank for ligand-based virtual screening
New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms
Adsorption of amino acids on MFI-type zeolite: DFT calculations and experimental results
pyPept: a python library to generate atomistic 2D and 3D representations of peptides
Transfer learning across different chemical domains: virtual screening of organic materials with deep learning models pretrained on small molecule and chemical reaction data
Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer
The Molecule Cloud - compact visualization of large collections of molecules
Double-head transformer neural network for molecular property prediction
A Branch-and-Bound approach for tautomer enumeration
Meat quality prediction using Raman spectroscopy and chemometrics
DeepSA: a deep-learning driven predictor of compound synthesis accessibility
Rational, computer-aided design of multi-target ligands
Application of the digital annealer unit in optimizing chemical reaction conditions for enhanced production yields
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
Rapid prediction of NMR spectral properties with quantified uncertainty
Chemogenomic approach to increase accuracy of QSAR modeling of inhibition activity against five major P450 isoforms
CheNER: a tool for the identification of chemical entities and their classes in biomedical literature
Status of the InChI algorithm and InChI trust
Luscus: molecular viewer and editor for MOLCAS
Extracting and connecting chemical structures from text sources using chemicalize.org
SMILES-based deep generative scaffold decorator for de-novo drug design
PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping
canSAR chemistry registration and standardization pipeline
Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes
Bingo from SciTouch LLC: chemistry cartridge for Oracle database
Uncovering molecular determinants of potency and binding affinity in hit compounds targeting FGF14/Nav1.6 complex
Implementing cheminformatics
Dimensionally reduced machine learning model for predicting single component octanol-water partition coefficients
The past, present and future of Scientific discourse
ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation
SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation
MolPrice: assessing synthetic accessibility of molecules based on market value
Predicting a small molecule-kinase interaction map: A machine learning approach
Consistent two-dimensional visualization of protein-ligand complex series
Surge: a fast open-source chemical graph generator
Using cheminformatics to predict cross reactivity of "designer drugs" to their currently available immunoassays
Kernel density estimation of CSD distributions - an application to knowledge based molecular optimisation
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection
SANCDB: an update on South African natural compounds and their readily available analogs
The topology of molecular representations and its influence on machine learning performance
BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts
WizePairZ: a novel algorithm to identify, encode, and exploit matched molecular pairs with unspecified cores in medicinal chemistry
iDrug: a web-accessible and interactive drug discovery and design platform
Comparison of ATP binding sites using structure-based similarity methods and molecular interaction fields
Mixture of experts for multitask learning in cardiotoxicity assessment
HAMdb: a database of human autophagy modulators with specific pathway and disease information
Systems chemistry: from chemical self-replication to trisoligo-based nanoconstruction
Exploring the known chemical space of the plant kingdom: insights into taxonomic patterns, knowledge gaps, and bioactive regions
Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning
Putting together the pieces: building a reaction-centric electronic lab notebook for mobile devices
Programmatic conversion of crystal structures into 3D printable files using Jmol
QuanDB: a quantum chemical property database towards enhancing 3D molecular representation learning
Structural diversity of biologically interesting datasets: a scaffold analysis approach
Utilizing maximal frequent itemsets and social network analysis for HIV data analysis
Structure-based machine learning screening identifies natural product candidates as potential geroprotectors
German Conference on Chemoinformatics 2010 - organizers' notes
MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment
Fleksy: a flexible approach to induced fit docking
Molecule database framework: a framework for creating database applications with chemical structure search capability
ChemicalTagger: A tool for semantic text-mining in chemistry
The use of 2D fingerprint methods to support the assessment of structural similarity in orphan drug legislation
Scaffold dependencies for halogen bonding: quantum mechanical investigation of nitrogen-bearing heterocycles
Get your chemistry right with KNIME
Scalable training of graph convolutional neural networks for fast and accurate predictions of HOMO-LUMO gap in molecules
Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids
Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules
Equivariant diffusion for structure-based de novo ligand generation with latent-conditioning
The kernel-weighted local polynomial regression (KwLPR) approach: an efficient, novel tool for development of QSAR/QSAAR toxicity extrapolation models
Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy
The protein flexibility in receptor-ligand docking simulations
Expanding and understanding metabolite space
Reply to "FAIR chemical structure in the Journal of Cheminformatics"
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining
The GMX-Plugin for the CELLmicrocosmos MembraneEditor
Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
Prediction of novel drug indications using network driven biological data prioritization and integration
Diversifying cheminformatics
The influence of solid state information and descriptor selection on statistical models of temperature dependent aqueous solubility
QSPR modeling of selectivity at infinite dilution of ionic liquids
ACID: a free tool for drug repurposing using consensus inverse docking strategy
Molecular generative model based on conditional variational autoencoder for de novo molecular design
MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning
DECIMER: towards deep learning for chemical image recognition
CWM global search - an internet search engine for the chemist
Cheminformatics approach to exploring and modeling trait-associated metabolite profiles
2D SIFt: a matrix of ligand-receptor interactions
Estimation of the applicability domain of kernel-based machine learning models for virtual screening
BuildAMol: a versatile Python toolkit for fragment-based molecular design
Verifying the fully "Laplacianised" posterior Naïve Bayesian approach and more
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning
Chemlistem: chemical named entity recognition using recurrent neural networks
Summarizing relationships between chemicals, genes, proteins, and diseases in PubChem using analysis of their co-occurrences in patents
Computer-assisted methods for molecular structure elucidation: realizing a spectroscopist's dream
Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture
Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s
3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors
SBE13, a newly identified inhibitor of inactive polo-like kinase 1
Balancing selectivity vs stability using molecular dynamics and umbrella sampling
Development of an open-source software for isomer enumeration
First steps towards semantic descriptions of electronic laboratory notebook records
The chemfp project
Efficient virtual high-content screening using a distance-aware transformer model
Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis
Novel pharmacological maps of protein lysine methyltransferases: key for target deorphanization
Large-scale virtual screening on public cloud resources with Apache Spark
An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package
Probabilistic metabolite annotation using retention time prediction and meta-learned projections
USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints
GTransCYPs: an improved graph transformer neural network with attention pooling for reliably predicting CYP450 inhibitors
A resource description framework (RDF) model of named entity co-occurrences in biomedical literature and its integration with PubChemRDF
Chemical pattern visualization in 2D - the SMARTSviewer
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification
LVPocket: integrated 3D global-local information to protein binding pockets prediction with transfer learning of protein structure classification
Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers
Probabilistic classifier: generated using randomised sub-sampling of the feature space
Entropy in specificity and thermodynamics of binding
Theoretical illustration of the effect of 1-ethyl-pyridinium trifluoroacetate ionic liquid in the enhancement of the Diels-Alder reaction of isoprene with acrylic acid
Condorcet and borda count fusion method for ligand-based virtual screening
Mol-CycleGAN: a generative model for molecular optimization
Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling
Adverse drug reactions triggered by the common HLA-B*57: 01 variant: virtual screening of DrugBank using 3D molecular docking
Flexible alignment in 3D and its applications
Development of a chemogenomics library for phenotypic screening
Backbone flexibility controls the activity and specificity of a protein-protein interface - specificity in snake venom metalloproteases (SVMPs)
Integrating QSAR modelling with reinforcement learning for Syk inhibitor discovery
Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem
Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning
A general approach for retrosynthetic molecular core analysis
Improved understanding of aqueous solubility modeling through topological data analysis
Ilm-NMR-P31: an open-access 31 P nuclear magnetic resonance database and data-driven prediction of 31 P NMR shifts
Chemozart: a web-based 3D molecular structure editor and visualizer platform
E-GuARD: expert-guided augmentation for the robust detection of compounds interfering with biological assays
Structure and thermodynamics of nonaqueous solvation by integral equation theory
Using structure- and Ligand-based pharmacophores as filters to discriminate Human Aryl Sulfotransferase 1A1 (SUL1A1) binders into substrates and inhibitors
Quantitative modeling of dose-response and drug combination based on pathway network
Potency-directed similarity searching using support vector machines
Nonadditivity in public and inhouse data: implications for drug design
The role of systems modeling in drug discovery and predictive health
MolNexTR: a generalized deep learning model for molecular image recognition
Molecular structure input on the web
Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections
Three stories about the conduct of science: Past, future, and present
PubChem3D: Biologically relevant 3-D similarity
Individual and collective human intelligence in drug design: evaluating the search strategy
DrugScorePPI for scoring protein-protein interactions: improving a knowledge-based scoring function by atomtype-based QSAR
VNFlow: integration of variational autoencoders and normalizing flows for novel molecular design
Composite multiscale chemical informatics for formulations: challenges and solutions
NaPLeS: a natural products likeness scorer - web application and database
A machine learning platform for the discovery of materials
Human-in-the-loop assisted de novo molecular design
In silico pK a prediction
4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening
Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on proteochemometric modelling
A big data approach to the ultra-fast prediction of DFT-calculated bond energies
NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores
Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow
NPBS Atlas: a comprehensive data resource for exploring the biological sources of natural products
MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design
Improving route development using convergent retrosynthesis planning
FusionCLM: enhanced molecular property prediction via knowledge fusion of chemical language models
Multi-PLI: interpretable multi-task deep learning model for unifying protein-ligand interaction datasets
Technical implications of new IUPAC elements in cheminformatics
INSARA: a new method for the analysis and visualization of Structure-Activity-Relationships
How the methodology of 3D structure preparation influences the quality of QSPR models?
CML: Evolution and design
Combatting over-specialization bias in growing chemical databases
"MS-Ready" structures for non-targeted high-resolution mass spectrometry screening studies
An investigation into pharmaceutically relevant mutagenicity data and the influence on Ames predictive potential
TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine
Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening
Improving integrative searching of systems chemical biology data using semantic annotation
High-throughput screening data generation, scoring and FAIRification: a case study on nanomaterials
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure
Selecting lines for spectroscopic (re)measurements to improve the accuracy of absolute energies of rovibronic quantum states
ABT-MPNN: an atom-bond transformer-based message-passing neural network for molecular property prediction
Correction: Enhanced Thompson sampling by roulette wheel selection for screening ultralarge combinatorial libraries
SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches
Smiles2Monomers: a link between chemical and biological structures for polymers
MOFGalaxyNet: a social network analysis for predicting guest accessibility in metal-organic frameworks utilizing graph convolutional networks
mineMS2: annotation of spectral libraries with exact fragmentation patterns
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models
Prediction-driven matched molecular pairs to interpret QSARs and aid the molecular optimization process
Development of machine learning classifiers to predict compound activity on prostate cancer cell lines
Building QSAR for HTS in vitro assays - a study for the prediction of Aryl hydrocarbon receptor activators
Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions
The dye-sensitized solar cell database
Understanding nanostructure formation from first principles
From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials
The influence of negative training set size on machine learning-based virtual screening
Correction: DecoyFinder, a tool for finding decoy molecules
From theory to experiment: transformer-based generation enables rapid discovery of novel reactions
InChI: connecting and navigating chemistry
Data-driven identification of structural alerts for mitigating the risk of drug-induced human liver injuries
Optimising chemical information workflows: integrating Reaxys - use cases and applications
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint
Correction: APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions
UMAP-based clustering split for rigorous evaluation of AI models for virtual screening on cancer cell lines
Efficient maximum common subgraph (MCS) searching of large chemical databases
Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery
AdductHunter: identifying protein-metal complex adducts in mass spectra
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation
Learning protein-ligand binding affinity with atomic environment vectors
Evaluating parameters for ligand-based modeling with random forest on sparse data sets
STOUT V2.0: SMILES to IUPAC name conversion using transformer models
Application of 3D atom pair map in an attention model for enhanced drug virtual screening
Molecular fragments chemoinformatics
Protein negative/positively cooperative binding to zwitterionic/anionic vesicles
Cavka - a new automatic pharmacophore elucidation method in progress
Docking and virtual screening of novel inhibitors for mono-ADP-ribosylating toxins
Computational methods for prediction of in vitro effects of new chemical structures
Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web
Statistical modeling of value distributions of similarity coefficients in virtual screening and its application to predicting fingerprint search performance
Structure-based classification and ontology in chemistry
An algorithm to identify functional groups in organic molecules