yusuke1997/dblp-id-title huggingface dataset:
BBB-PEP-prediction: improved computational model for identification of blood-brain barrier peptides using blending position relative composition specific features and ensemble modeling
Advantages of two quantum programming platforms in quantum computing and quantum chemistry
Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data
BitterMatch: recommendation systems for matching molecules with bitter taste receptors
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design
GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations
GEN: highly efficient SMILES explorer using autodidactic generative examination networks
The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets
Bloom filters for molecules
Matched pairs demonstrate robustness against inter-assay variability
InChI - the worldwide chemical structure identifier standard
A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening
Dynamic information system for small molecules
Packaging free software chemistry programs in Debian GNU/Linux: past, present and future
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management
Modeling framework for isotopic labeling of heteronuclear moieties
Efficient extraction of canonical spatial relationships using a recursive enumeration of k-subsets
Correction: Global reactivity models are impactful in industrial synthesis applications
Improving drug-induced liver injury prediction using graph neural networks with augmented graph features from molecular optimisation
Personalized information spaces: improved access to chemical digital libraries
Winnow based identification of potent hERG inhibitors in silico: comparative assessment on different datasets
International chemical identifier for reactions (RInChI)
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification
Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models
Collaborative decision support and documentation in chemical safety with KnowSEC
Representation and searching of biomolecules
Are the physicochemical properties of antibacterial compounds really different from other drugs?
Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities
Finding unusual peptides on the internet using plain three letter sequence codes
Scaffold Hunter: a comprehensive visual analytics framework for drug discovery
Studies on the mechanism of the lactide polymerization with highly active zinc guanidine catalysts
Automated simultaneous assignment of bond orders and formal charges
ILPC: simple chemometric tool supporting the design of ionic liquids
Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature
ADMET evaluation in drug discovery: 21. Application and industrial validation of machine learning algorithms for Caco-2 permeability prediction
MORTAR: a rich client application for in silico molecule fragmentation
Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents
Prediction of Pt, Ir, Ru, and Rh complexes light absorption in the therapeutic window for phototherapy using machine learning
The semantics of Chemical Markup Language (CML) for computational chemistry: CompChem
Relative molecule self-attention transformer
Novel binding pocket descriptors based on DrugScore potential fields encoded by 3D Zernike descriptors
Combining SFCscore with Random Forests leads to improved affinity prediction for protein-ligand complexes
TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry
Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization
A new method for the comparison of 1 H NMR predictors based on tree-similarity of spectra
Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations
SYBA: Bayesian estimation of synthetic accessibility of organic compounds
Open Bibliography for Science, Technology, and Medicine
EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances
Profiling and analysis of chemical compounds using pointwise mutual information
Basic primitives for molecular diagram sketching
Towards targeting protein-protein interfaces with small molecules
A flexible-hydrogen interaction model for protein-ligand docking
A molecule perturbation software library and its application to study the effects of molecular design constraints
A beginner's approach to deep learning applied to VS and MD techniques
Enhancing molecular property prediction through data integration and consistency assessment
Application of Structural Interaction Fingerpints (SIFts) into post-docking analysis - insight into activity and selectivity
Prediction of blood-brain barrier and Caco-2 permeability through the Enalos Cloud Platform: combining contrastive learning and atom-attention message passing neural networks
Hilbert-curve assisted structure embedding method
The ChEMBL database as linked open data
Get the best from substructure mining
Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors
Investigation of the structure-odor relationship using a Transformer model
Cross-project HTS-datamining
EasyDock: customizable and scalable docking tool
Molecular optimization by capturing chemist's intuition using deep neural networks
Interface-aware molecular generative framework for protein-protein interaction modulators
StreamChol: a web-based application for predicting cholestasis
Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids
Pocket Crafter: a 3D generative modeling based workflow for the rapid generation of hit molecules in drug discovery
Openness as infrastructure
One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data
Flame: an open source framework for model development, hosting, and usage in production environments
A computational method to facilitate structure-activity relationship transfer
AMBIT RESTful web services: an implementation of the OpenTox application programming interface
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands
CavKA HYBRID - between hard spheres and Gaussians
mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATEX code
Mining basic active structures from a large-scale database
EDock: blind protein-ligand docking by replica-exchange monte carlo simulation
Modelling dissociation constants of organic acids by local molecular parameters
Enhancing of chemical compound and drug name recognition using representative tag scheme and fine-grained tokenization
VitroBert: modeling DILI by pretraining BERT on in vitro data
Quantum chemical calculations on a unified pH scale for all phases
Building an R&D chemical registration system
Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain
Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)
Large scale chemical patent mining with UIMA and UNICORE
An activity canyon characterization of the pharmacological topography
Target enhanced 2D similarity search by using explicit biological activity annotations and profiles
CACTI: an in silico chemical analysis tool through the integration of chemogenomic data and clustering analysis
Unveiling polyphenol-protein interactions: a comprehensive computational analysis
HighFold-MeD: a Rosetta distillation model to accelerate structure prediction of cyclic peptides with backbone N-methylation and d-amino acids
Methodology of aiQSAR: a group-specific approach to QSAR modelling
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data
Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics
Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method
Relating GPCRs pharmacological space based on ligands chemical similarities
Neural SHAKE: geometric constraints in neural differential equations
Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field
Optimized SQE atomic charges for peptides accessible via a web application
Quantum-mechanics-based molecular interaction fields for 3D-QSAR
Improvements in docking scoring functions: the physics-based perspective
Correction to: Optimized SQE atomic charges for peptides accessible via a web application
Aromatic clusters in protein-protein and protein-drug complexes
Updating existing QSAR models: selection and weighting of new data
Molmil: a molecular viewer for the PDB and beyond
Integrating synthetic accessibility with AI-based generative drug design
Consensus Diversity Plots: a global diversity analysis of chemical libraries
Classification of battery compounds using structure-free Mendeleev encodings
Integrating logic-based machine learning and virtual screening to discover new drugs
Processing binding data using an open-source workflow
Dragon exploration system on marine sponge compounds interactions
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures
Review of techniques and models used in optical chemical structure recognition in images and scanned documents
Efficient decoy selection to improve virtual screening using machine learning models
Prediction model for chemical explosion consequences via multimodal feature fusion
Integration of chemical information with protein sequences and 3D structures
piscesCSM: prediction of anticancer synergistic drug combinations
DBPP-Predictor: a novel strategy for prediction of chemical drug-likeness based on property profiles
Estimating the synthetic accessibility of molecules with building block and reaction-aware SAScore
VSFlow: an open-source ligand-based virtual screening tool
Predictive classification models and targets identification for betulin derivatives as Leishmania donovani inhibitors
ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
Modeling of molecular atomization energies using machine learning
A fingerprints based molecular property prediction method using the BERT model
Surfactant representation using COSMO screened charge density for adsorption isotherm prediction using Physics-Informed Neural Network (PINN)
The Spectral Game: leveraging Open Data and crowdsourcing for education
Simulating the drug discovery pipeline: a Monte Carlo approach
Towards reproducible computational drug discovery
Pmf-cpi: assessing drug selectivity with a pretrained multi-functional model for compound-protein interactions
Nipah Virus Inhibitor Knowledgebase (NVIK): a combined evidence approach to prioritise small molecule inhibitors
LigninGraphs: lignin structure determination with multiscale graph modeling
OMG: open molecule generator
Large language models open new way of AI-assisted molecule design for chemists
inSARa: intuitive single-target (large-scale) SAR interpretation and multi-target cross-reactivity analysis
Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge
A neural network approach to chemical and gene/protein entity recognition in patents
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets
Force field-inspired transformer network assisted crystal density prediction for energetic materials
MORT: a powerful foundational library for computational biology and CADD
A multi-label approach to target prediction taking ligand promiscuity into account
PubChem3D: a new resource for scientists
Peptide lineup against Gram-negative bacterial infection - first-in-class peptide inhibitor of H. pylori HtrA
A general model for predicting enzyme functions based on enzymatic reactions
Neural network based classification of acute toxicity of phthalate esters to fathead minnow
InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism
AMADAR: a python-based package for large scale prediction of Diels-Alder transition state geometries and IRC path analysis
Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia
Picking out polymorphs: H-bond prediction and crystal structure stability
Proteochemometric modeling in a Bayesian framework
Mining Chemical Libraries with "Screening Assistant 2"
Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes
Implicit-descriptor ligand-based virtual screening by means of collaborative filtering
AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions
Use of structure-activity landscape index curves and curve integrals to evaluate the performance of multiple machine learning prediction models
Virtual screening for plant PARP inhibitors - what can be learned from human PARP inhibitors?
A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility
Chemical datuments as scientific enablers
Go with the flow and accessorize your drugs
Leveraging AI to explore structural contexts of post-translational modifications in drug binding
Learning symmetry-aware atom mapping in chemical reactions through deep graph matching
Review of "Contemporary computer-assisted approaches to molecular structure elucidation (new developments in NMR)" by Mikhail E Elyashberg, Antony Williams and Kirill Blinov
Application of 3D Zernike descriptors to shape-based ligand similarity searching
Capturing mixture composition: an open machine-readable format for representing mixed substances
Adverse drug reactions triggered by the common HLA-B*57: 01 variant: a molecular docking study
Multiple conformational states in retrospective virtual screening - homology models vs. crystal structures: beta-2 adrenergic receptor case study
OCHEM - on-line CHEmical database & modeling environment
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty
Dingo: 2D molecule and reaction structural formula rendering library
Predicting target profiles with confidence as a service using docking scores
Fifteen years of ChEMBL and its role in cheminformatics and drug discovery
Exploring QSAR models for activity-cliff prediction
Correction: Retrosynthetic crosstalk between single-step reaction and multi-step planning
Virtual screening workflow for glycogen synthase kinase 3β inhibitors: convergence of ligand-based and structure-based approaches
A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space
Tabu search based global optimization algorithms for problems in computational chemistry
Comparative evaluation of methods for the prediction of protein-ligand binding sites
Terminology spectrum analysis of natural-language chemical documents: term-like phrases retrieval routine
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations
Paths to Cheminformatics: Q&A with Norberto Sánchez-Cruz and Emma Schymanski
Helping to improve the practice of cheminformatics
Insights into binding events of GABA- and Tiagabine- analogues in the Gamma-Aminobutyric Acid Transporter 1 by means of Molecular Modelling
Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data
Enhancing chemical synthesis: a two-stage deep neural network for predicting feasible reaction conditions
Twitter integration of chemistry software tools
IDSM ChemWebRDF: SPARQLing small-molecule datasets
Ushering the Cactvs Toolkit into the Python Age (without breaking the legacy)
Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules
Publishing neural networks in drug discovery might compromise training data privacy
Multimodal data fusion for supervised learning-based identification of USP7 inhibitors: a systematic comparison
Cycle-configuration descriptors: a novel graph-theoretic approach to enhancing molecular inference
SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer
DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning
S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands
Enhancing multi-task in vivo toxicity prediction via integrated knowledge transfer of chemical knowledge and in vitro toxicity information
A path to next-generation reproducibility in cheminformatics
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra
TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data
Stereochemically-aware bioactivity descriptors for uncharacterized chemical compounds
Correction to: Interoperable chemical structure search service
MolCompass: multi-tool for the navigation in chemical space and visual validation of QSAR/QSPR models
Insights into predicting small molecule retention times in liquid chromatography using deep learning
LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data
Statistical filtering for NMR based structure generation
Accelerating turbo similarity searching in chemoinformatics on multicore and GPU platforms
A possible extension to the RInChI as a means of providing machine readable process data
Feature combination networks for the interpretation of statistical machine learning models: application to Ames mutagenicity
The PubChem chemical structure sketcher
Continuous symmetry and chirality measures: approximate algorithms for large molecular structures
Activity landscape image analysis using convolutional neural networks
Generalizable, fast, and accurate DeepQSPR with fastprop
Consensus queries in ligand-based virtual screening experiments
Automatic procedure for generating symmetry adapted wavefunctions
A look back at a pilot of the citation typing ontology
DrugDiff: small molecule diffusion model with flexible guidance towards molecular properties
From chemical shift data through prediction to assignment and NMR LIMS - multiple functionalities of nmrshiftdb2
GCC2011 - 25 years of computational chemistry meetings
Review of "Statistical Modelling of Molecular Descriptors in QSAR/QSPR" by Matthias Dehmer, Kurt Varmuza, and Danail Bonchev
MolPROP: Molecular Property prediction with multimodal language and graph fusion
CardioGenAI: a machine learning-based framework for re-engineering drugs for reduced hERG liability
Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment
In silico identification of novel PKC βII inhibitors: ligand and receptor based pharmacophore modeling, virtual screening, and molecular dynamics study
Achieving well-informed decision-making in drug discovery: a comprehensive calibration study using neural network-based structure-activity models
Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics
PUResNet: prediction of protein-ligand binding sites using deep residual neural network
Extended study on atomic featurization in graph neural networks for molecular property prediction
Fragment docking supported by NMR shift perturbations
Open-source platform to benchmark fingerprints for ligand-based virtual screening
Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools
Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES
Interpretable correlation descriptors for quantitative structure-activity relationships
Organization of GC/MS and LC/MS metabolomics data into chemical libraries
The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC-TOF MS metabolome samples
Open access: changing the way chemistry is published
Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C 10 E 4 /water mixture with lamellar bilayer formation
In-silico design of computational nucleic acids for molecular information processing
Improving structural similarity based virtual screening using background knowledge
Sequence-based prediction of protein binding regions and drug-target interactions
Approaching the limits: scoring functions for affinity prediction
Determination of selected cetyltrimethylammonium halide parameters by molecular modeling. Study of their adsorption on montmorillonite
Configurable web-services for biomedical document annotation
Free-Wilson in the 21st Century - evolution of a versatile toolkit for SAR analysis
The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers
chemmodlab: a cheminformatics modeling laboratory R package for fitting and assessing machine learning models
Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications
PubChem atom environments
Novel applications of Machine Learning in cheminformatics
COSMOsim3D for drug-similarity, alignment, and molecular field analysis
Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling
Explaining and avoiding failure modes in goal-directed generation of small molecules
The algebraic extended atom-type graph-based model for precise ligand-receptor binding affinity prediction
Exploring non-linear distance metrics in the structure-activity space: QSAR models for human estrogen receptor
Contrastive explanations for machine learning predictions in chemistry
Modeling enzyme-ligand binding in drug discovery
Nanodesigner: resolving the complex-CDR interdependency with iterative refinement
DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning
9th German Conference on Chemoinformatics
Benchmarks for interpretation of QSAR models
Improving reproducibility and reusability in the Journal of Cheminformatics
Investigation of pharmacological mechanism of natural product using pathway fingerprints similarity based on "drug-target-pathway" heterogenous network
The Open Spectral Database: an open platform for sharing and searching spectral data
SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides
OrChem: an open source chemistry search engine for Oracle
PubChem synonym filtering process using crowdsourcing
Shinyscreen: mass spectrometry data inspection and quality checking utility
Mixtures, metabolites, ionic liquids: a new measure to evaluate similarity between complex chemical systems
Computational nanotechnology for functional coatings
Reproducible MS/MS library cleaning pipeline in matchms
PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction