yusuke1997/dblp-id-title huggingface dataset:
Experimental validation of in silico target predictions on synergistic protein targets
Identification of host interactions for phenotypic antimalarial hits
In silico characterization of the motor subunit of the e.coli. restriction-modification system EcoR1241
PUG-View: programmatic access to chemical annotations integrated in PubChem
Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles
Evolutionary design of selective adenosine receptor ligands
A comprehensive landscape of AI applications in broad-spectrum drug interaction prediction: a systematic review
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction
RLSuccSite: succinylation sites prediction based on reinforcement learning dynamic with balanced reward mechanism and three-peaks enhanced method for physicochemical property scores
Algorithm-supported, mass and sequence diversity-oriented random peptide library design
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis
Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin
ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK)
Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders
Data governance in predictive toxicology: A review
The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data
Assessing the information content of structural and protein-ligand interaction representations for the classification of kinase inhibitor binding modes via machine learning and active learning
QSAR DataBank - an approach for the digital organization and archiving of QSAR model information
An integrated quantitative structure and mechanism of action-activity relationship model of human serum albumin binding
Evaluation of reinforcement learning in transformer-based molecular design
TCMSP: a database of systems pharmacology for drug discovery from herbal medicines
In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences
Development of scoring-assisted generative exploration (SAGE) and its application to dual inhibitor design for acetylcholinesterase and monoamine oxidase B
LogD7.4 prediction enhanced by transferring knowledge from chromatographic retention time, microscopic pKa and logP
New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0
Using Jupyter Notebooks for re-training machine learning models
FluoBase: a fluorinated agents database
Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers
QSPR designer - employ your own descriptors in the automated QSAR modeling process
StreaMD: the toolkit for high-throughput molecular dynamics simulations
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets
Adaptive language model training for molecular design
Mechanistic studies on the ring-opening polymerisation of D, L-lactide with zinc guanidine complexes
Small Molecule Subgraph Detector (SMSD) toolkit
EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency
Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta
Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets
Hit series selection in noisy HTS data: clustering techniques, statistical tests and data visualisations
Can human experts predict solubility better than computers?
Robust optimization of SVM hyperparameters in the classification of bioactive compounds
CheS-Mapper - Chemical Space Mapping and Visualization in 3D
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening
How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening
WikiHyperGlossary (WHG): an information literacy technology for chemistry documents
TB-IECS: an accurate machine learning-based scoring function for virtual screening
Accurate prediction of protein-ligand interactions by combining physical energy functions and graph-neural networks
SANCDB: a South African natural compound database
Enhanced ranking of PknB Inhibitors using data fusion methods
A retrosynthetic analysis algorithm implementation
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists
Facing the challenges of computational target prediction
ChemSpider - building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry
Automatic pharmacophore model generation using weighted substructure assignments
The semantic architecture of the World-Wide Molecular Matrix (WWMM)
Extraction of useful bioisostere replacments from the PDB
The nature of ligand efficiency
Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath
Automatic molecular fragmentation by evolutionary optimisation
GPURFSCREEN: a GPU based virtual screening tool using random forest classifier
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications
Correction: Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development
Machine learning for the prediction of molecular dipole moments obtained by density functional theory
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop
Inferring multi-target QSAR models with taxonomy-based multi-task learning
Subgrapher: visual fingerprinting of chemical structures
The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network
Automated compound classification using a chemical ontology
Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock
Quantitative estimation of pesticide-likeness for agrochemical discovery
CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration
Bitter peptide prediction using graph neural networks
Linked open drug data for pharmaceutical research and development
Applications of the InChI in cheminformatics with the CDK and Bioclipse
RAIChU: automating the visualisation of natural product biosynthesis
Patch seriation to visualize data and model parameters
Rescoring of docking poses using force field-based methods
Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1
ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules
An efficient computer-aided structural elucidation strategy for mixtures using an iterative dynamic programming algorithm
Computational analysis and predictive modeling of small molecule modulators of microRNA
Open-source QSAR models for pKa prediction using multiple machine learning approaches
Designing optimized drug candidates with Generative Adversarial Network
DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning
SciData: a data model and ontology for semantic representation of scientific data
SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs
DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism
Detecting drug communities and predicting comprehensive drug-drug interactions via balance regularized semi-nonnegative matrix factorization
Fate-tox: fragment attention transformer for E(3)-equivariant multi-organ toxicity prediction
Erratum to: ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics
Virtual screening and in silico design of novel inhibitors of bacterial lectins
The published role of artificial intelligence in drug discovery and development: a bibliometric and social network analysis from 1990 to 2023
Post-acquisition filtering of salt cluster artefacts for LC-MS based human metabolomic studies
Nemesis - a molecular modeling package
Extended graph-based models for enhanced similarity retrieval in Cavbase
SIA: a scalable interoperable annotation server for biomedical named entities
Analysis of metabolites in human gut: illuminating the design of gut-targeted drugs
Expanding natural product chemistry resources at the EBI
Large-scale comparison of machine learning methods for profiling prediction of kinase inhibitors
Pretraining graph transformers with atom-in-a-molecule quantum properties for improved ADMET modeling
Searching for bioactive conformations of drug-like ligands with current force fields: how good are we?
Virtual screening by high-throughput docking using hydrogen bonding constraints for targeting a protein-protein interface in M. tuberculosis
Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation
Paths to cheminformatics: Q&A with Ann M. Richard
Using informative features in machine learning based method for COVID-19 drug repurposing
spyrmsd: symmetry-corrected RMSD calculations in Python
Estimation of diffusion coefficients from voltammetric signals by support vector and gaussian process regression
Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information
Computational prediction of heterogeneous interface properties at the atomic level
InflamNat: web-based database and predictor of anti-inflammatory natural products
Similarity-based pairing improves efficiency of siamese neural networks for regression tasks and uncertainty quantification
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores
Dualsteric modulators of the M2 muscarinic acetylcholine receptor
Molecular generation by Fast Assembly of (Deep)SMILES fragments
Robustness under parameter and problem domain alterations of Bayesian optimization methods for chemical reactions
Prediction of the water solubility by a graph convolutional-based neural network on a highly curated dataset
InChI, the IUPAC International Chemical Identifier
An open source chemical structure curation pipeline using RDKit
QBMG: quasi-biogenic molecule generator with deep recurrent neural network
Chemical ontologies: what are they, what are they for and what are the challenges
SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors
Constraint counting on RNA and ribosomal structures: linking flexibility and function
Annotation and detection of drug effects in text for pharmacovigilance
Supercell program: a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals
MetFrag relaunched: incorporating strategies beyond in silico fragmentation
Dissecting the role of guanidine copper complexes in atom transfer radical polymerization by density functional theory
Barlow Twins deep neural network for advanced 1D drug-target interaction prediction
Jmol SMILES and Jmol SMARTS: specifications and applications
Accelerating the inference of string generation-based chemical reaction models for industrial applications
Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features
Identifying uncertainty in physical-chemical property estimation with IFSQSAR
The specification game: rethinking the evaluation of drug response prediction for precision oncology
Mordred: a molecular descriptor calculator
Simulation of transport processes and chemical reactions in building materials
DECIMER 1.0: deep learning for chemical image recognition using transformers
Higher education in chemoinformatics: achievements and challenges
PINNED: identifying characteristics of druggable human proteins using an interpretable neural network
HTS explorer
Usage and applications of Semantic Web techniques and technologies to support chemistry research
Estimation of acute oral toxicity in rat using local lazy learning
Be aware of overfitting by hyperparameter optimization!
Development and evaluation of two-parameter linear free energy models for the prediction of human skin permeability coefficient of neutral organic chemicals
Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases
Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design
Large-scale ligand-based predictive modelling using support vector machines
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology
Group graph: a molecular graph representation with enhanced performance, efficiency and interpretability
Efficient conformational ensemble generation of protein-bound peptides
Membrane simulation analysis using Voronoi tessellation
The Human Omnibus of Targetable Pockets
DGet! An open source deuteration calculator for mass spectrometry data
Transformer-CNN: Swiss knife for QSAR modeling and interpretation
Maximum common property: a new approach for molecular similarity
MycPermCheck: the Mycobacterium tuberculosis permeability prediction tool for small molecules
Revisiting the dataflow principle for chemical information processing
Virtual screening using structure-based consensus pharmacophore models and ensemble docking based on MD-generated conformations
PriaXplore ® - a novel technology platform for the identification of small molecule modulators of protein-protein interactions
Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm
eTOXlab, an open source modeling framework for implementing predictive models in production environments
Chemical named entities recognition: a review on approaches and applications
An interpretable deep geometric learning model to predict the effects of mutations on protein-protein interactions using large-scale protein language model
LAGNet: better electron density prediction for LCAO-based data and drug-like substances
KRIPO - a structure-based pharmacophores approach explains polypharmacological effects
Enhancing atom mapping with multitask learning and symmetry-aware deep graph matching
High throughput in-silico screening against flexible protein receptors
Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs)
Predicting the mechanism of phospholipidosis
Chemical classification program synthesis using generative artificial intelligence
Advanced machine learning for innovative drug discovery
Fragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding-based methodology
TorsionAnalyzer: exploring conformational space
The influence of the inactives subset generation on the performance of machine learning methods
Discovery of novel TLR modulators by Molecular Modeling and Virtual Screening
Simultaneously improving accuracy and computational cost under parametric constraints in materials property prediction tasks
Universal nanohydrophobicity predictions using virtual nanoparticle library
PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
"Ask Ernö": a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra
CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer
Deep scaffold hopping with multimodal transformer neural networks
From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language
Automated molecular structure segmentation from documents using ChemSAM
PretoxTM: a text mining system for extracting treatment-related findings from preclinical toxicology reports
Ligand-based virtual screening interface between PyMOL and LiSiCA
Probabilistic generative transformer language models for generative design of molecules
http://Mcule.com: a public web service for drug discovery
InCHlib - interactive cluster heatmap for web applications
A next-generation chemistry database cartridge
Target prediction utilising negative bioactivity data covering large chemical space
Consistency of sugar structures and their annotation in the PDB
Ensemble docking revisited
InChIKey collision resistance: an experimental testing
PURE: policy-guided unbiased REpresentations for structure-constrained molecular generation
Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization
Brute-force pharmacophore assessment and scoring with Open3DQSAR
Grand challenges for cheminformatics
A BERT-based pretraining model for extracting molecular structural information from a SMILES sequence
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations
Molecular bioactivity extrapolation to novel targets by support vector machines
Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development
Correction: A transformer based generative chemical language AI model for structural elucidation of organic compounds
CARTESIUS: a group function based toolkit for hybrid molecular modelling
Correction to: A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications
SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering
Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation
Exploiting solvent effects in drug design and optimization
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity
Classification of CYP450 1A2 inhibitors using PubChem data
DACS: from compound collections to rationally designed HTS library
Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases
A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles
ChemProps: A RESTful API enabled database for composite polymer name standardization
Semantics vs. statistics in chemical markup
LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds
Biomaterialcoatings - a challenging task studied by the molecular fragment dynamics
Making sure there's a "give" associated with the "take": producing and using open-source software in big pharma
One chiral fingerprint to find them all
Ensemble completeness in conformer sampling: the case of small macrocycles
Deterministic clustering of the available chemical space
Diagnostic of tautomer behaviour on QSAR models and AM1 optimisation
A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications
Deep learning-driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles
Computational pharmaceutical materials science
A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature
The development of the generative adversarial supporting vector machine for molecular property generation
Clc-db: an open-source online database of chiral ligands and catalysts
ChemScanner: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files
Benchmarking molecular conformer augmentation with context-enriched training: graph-based transformer versus GNN models
A 3D-QSAR model for cannabinoid receptor (CB2) ligands derived from aligned pharmacophors
Recognition of chemical entities: combining dictionary-based and grammar-based approaches
ProjFusNet: deep neural network for peptide precursor prediction using projection-fused protein language model and structural features
Reconstruction of lossless molecular representations from fingerprints
PubChem3D: Diversity of shape
GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts
Resource description framework technologies in chemistry
Modeling of non-additive mixture properties using the Online CHEmical database and Modeling environment (OCHEM)
Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds
The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability
Mechanistic DFT studies - helicate-type complexes with different alcylic spacers
Molecular identification via molecular fingerprint extraction from atomic force microscopy images
8th German Conference on Chemoinformatics
Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions
Predicting volume of distribution with decision tree-based regression methods using predicted tissue: plasma partition coefficients
Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
FAIR chemical structures in the Journal of Cheminformatics
An algorithm to classify homologous series within compound datasets
Protein target similarity is positive predictor of in vitro antipathogenic activity: a drug repurposing strategy for Plasmodium falciparum
Chemical reaction network knowledge graphs: the OntoRXN ontology
Alphappimi: a comprehensive deep learning framework for predicting PPI-modulator interactions
Beryllium 10 : a free and simple tool for creating and managing group safety data sheets
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping
Quantifying the shifts in physicochemical property space introduced by the metabolism of small organic molecules
ParaDockS - an open-source framework for molecular docking: implementation of target-class-specific scoring methods
Implementation of a soft grading system for chemistry in a Moodle plugin
Splitting chemical structure data sets for federated privacy-preserving machine learning
Using Pareto points for model identification in predictive toxicology
Enhancing molecular property prediction with quantized GNN models
Measuring Chemical LLM robustness to molecular representations: a SMILES variation-based framework
AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization
Design of dual ligands using excessive pharmacophore query alignment
Implementation of an open chemistry knowledge base with a Semantic Wiki
De novo design of molecular wires with optimal properties for solar energy conversion
MoSGrid - a molecular simulation grid as a new tool in computational chemistry, biology and material science
A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data