yusuke1997/dblp-id-title huggingface dataset:
Predicting Elimination of Small-Molecule Drug Half-Life in Pharmacokinetics Using Ensemble and Consensus Machine Learning Methods
Automatic identification and manipulation of receptor sites in proteins. 2. Electrostatic complementarity analysis for the evaluation and selection of candidate ligand receptor sites
Prediction of Anti-HIV-1 Activity of a Series of Tetrapyrrole Molecules
VSMP: A Novel Variable Selection and Modeling Method Based on the Prediction
Pearson-type I Distribution Function for Polydisperse Polymer Systems. Molar Mass Distribution
A Versatile Structural Domain Analysis Server Using Profile Weight Matrices
Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening
Analysis of the Registry of Toxic Effects of Chemical Substances (RTECS) Files and Conversion of the Data in These Files for Input to the Environmental Chemicals Data and Information Network (ECDIN)
Information and Emotion: The Emergent Affective Paradigm in Information Behavior Research and Theory
MRP.py: A Parametrizer of Post-Translationally Modified Residues
Structural Investigations of Acridine Derivatives by CoMFA and CoMSIA Reveal Novel Insight into Their Structures toward DNA G-Quadruplex Mediated Telomerase Inhibition and Offer a Highly Predictive 3D-Model for Substituted Acridines
PM3(tm) Analysis of Transition-Metal Complexes
CHEMICS-F: A Computer Program System for Structure Elucidation of Organic Compounds
Faces of Contemporary CryoEM Information and Modeling
Three Descriptor Model Sets a High Standard for the CSAR-NRC HiQ Benchmark
Molecular Quantum Similarity-Based QSARs for Binding Affinities of Several Steroid Sets
Discovery of Tetrahydroisoquinoline-Based SARS-CoV-2 Helicase Inhibitors with Iterative, Deep Learning-Enhanced Virtual Screening
Impact of Deamidation on the Structure and Function of Antiapoptotic Bcl-xL
Assessing Uncertainty in Machine Learning for Polymer Property Prediction: A Benchmark Study
Advanced Biological and Chemical Discovery (ABCD): Centralizing Discovery Knowledge in an Inherently Decentralized World
Extremal Mono-q-polyhexes
Agonists and Antagonists Show Different Unbinding Paths from the TLR8 Receptor
Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation
Leveraging Language Model Multitasking To Predict C-H Borylation Selectivity
Virtual Affinity Fingerprints for Target Fishing: A New Application of Drug Profile Matching
A pharmaceutical information manager's viewpoint on R&D information resource management
Investigation on an Orientation and Interaction Energy of the Water Molecule in the HIV-1 Reverse Transcriptase Active Site by Quantum Chemical Calculations
Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method
On Combining Recursive Partitioning and Simulated Annealing To Detect Groups of Biologically Active Compounds
HydraMap v.2: Prediction of Hydration Sites and Desolvation Energy with Refined Statistical Potentials
EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation
Virtual Screening Against Carbohydrate-Binding Proteins: Evaluation and Application to BacterialBurkholderia ambifariaLectin
Benchmarking 3D Structure-Based Molecule Generators
Regarding Enumeration of Molecular Isomers
Are There Signed Cospectral Graphs?
Water-Based Pharmacophore Modeling in Kinase Inhibitor Design: A Case Study on Fyn and Lyn Protein Kinases
Toward Machine Learning Electrospray Ionization Sensitivity Prediction for Semiquantitative Lipidomics in Stem Cells
Novel Approach to the Analysis of Chemical Third-Order Data
Cavity Characterization in Supramolecular Cages
Structural Flexibility of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitor: 9-Cl TIBO as Explained by Potential Energy Surface and 13 C and 1 H NMR Calculations, Based on ab initio and Density Functional Study
A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments
Evolution of Alchemical Free Energy Methods in Drug Discovery
Molecular Mechanism of Ca 2+ in the Allosteric Regulation of Human Parathyroid Hormone Receptor-1
A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B
Correction to A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations
Construction and Use of Fragment-Augmented Molecular Hasse Diagrams
Improving the Silicon Interactions of GFN-xTB
Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway
Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein-Ligand Interactions
Generation and enumeration of carbon skeletons
Micro computer software. 1. After FORTRAN
Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces
Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation
Reference Literature to the Critical Properties of Aqueous Electrolyte Solutions
Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein-Ligand Interactions
Conformational Dynamics in Corynebacterium glutamicum Diaminopimelate Epimerase: Insights from Ligand Parameterization, Atomistic Simulation, and Markov State Modeling
Mining the Dynamical Properties of Substrate and FAD Binding Pockets of LSD1: Hints for New Inhibitor Design Direction
Do the Neighboring Residues in a Polypeptide Affect the Electron Distribution of an Amino Acid Significantly? A Quantitative Study Using the Quantum Theory of Atoms in Molecules (QTAIM)
HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales
OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions
Finding Multiactivity Substructures by Mining Databases of Drug-Like Compounds
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design
A Multimodal Drug-Target Affinity Prediction Framework with Pretrained Models and Hierarchical Graph Transformer
Time-Split Cross-Validation as a Method for Estimating the Goodness of Prospective Prediction
A spatial database manager for a generic image-understanding system
McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms
Central Patents Index Chemical Code: a user's viewpoint
Structure-property relationship in sweeteners
PAD programming and its application in chemistry
A Chemical Index Inspired by Biological Plastic Evolution: Valence-Isoelectronic Series of Aromatics
Small Molecule NS11021 Promotes BK Channel Activation by Increasing Inner Pore Hydration
Toward an Alternative Hardness Kernel Matrix Structure in the Electronegativity Equalization Method (EEM)
Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design
The Quest for Bioisosteric Replacements
Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum
Identification of Novel Non-Hydroxamate Anthrax Toxin Lethal Factor Inhibitors by Topomeric Searching, Docking and Scoring, and in Vitro Screening
Reaction-MQL: Line Notation for Functional Transformation
Predicting the Dynamic Interaction of Intrinsically Disordered Proteins
Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions
Perspectives and criteria for chemical information instruction
Process Design Principles: Synthesis, Analysis, and Evaluation By Warren D. Seider, J. D. Seader, and Daniel R. Lewin. Wiley: New York, 1999, 824 pp, ISBN 0-471-24312-4
Simulation Analysis of Experimental Design Strategies for Screening Random Compounds as Potential New Drugs and Agrochemicals
EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions
In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy
Image2InChI: Automated Molecular Optical Image Recognition
On the Use of 1 H and 13 C 1D NMR Spectra as QSPR Descriptors
The CAS ONLINE search system. 1. General system design and selection, generation, and use of search screens
Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy
Improving Classical Substructure-Based Virtual Screening to Handle Extrapolation Challenges
Refining the Trapping of Therapeutic Agent Silybin A in Functionalized β- and γ-Cyclodextrin Cavitands for Improved Supramolecular Complexation
Would the Pseudocoordination Centre Method Be Appropriate To Describe the Geometries of Lanthanide Complexes?
Molecular Environment-Specific Atomic Charges Improve Binding Affinity Predictions of SAMPL5 Host-Guest Systems
Identification of High-Reliability Regions of Machine Learning Predictions Based on Materials Chemistry
Augmenting Chemical Databases for Atomistic Machine Learning by Sampling Conformational Space
A periodic table for polycyclic aromatic hydrocarbons. Isomer enumeration of fused polycyclic aromatic hydrocarbons. Part I
IRA: A Shape Matching Approach for Recognition and Comparison of Generic Atomic Patterns
Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM
Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns
FOCUS-DB: An Online Comprehensive Database on Food Additive Safety
Network-Based Methods and Their Applications in Drug Discovery
MAGIC: A Multimodal Adaptive GRN Inference Constructor
Analysis of Calcium, Oxalate, and Citrate Interaction in Idiopathic Calcium Urolithiasis in Children
Topological statistics on a large structural file
MolAI: A Deep Learning Framework for Data-Driven Molecular Descriptor Generation and Advanced Drug Discovery Applications
Oriented 2-Cell Embeddings of a Graph and Their Symmetry Classification: Generating Algorithms and Case Study of the Möbius-Kantor Graph
Studies on the Interactions between β 2 Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations
Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System (BDDCS)
Deep Generative Models in De Novo Drug Molecule Generation
Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease
Computer Aided Method for Chemical Structure Elucidation Using Spectral Databases and 13C NMR Correlation Tables
Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins
Hydrophobic/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation
Molecular Design for Cardiac Cell Differentiation Using a Small Data Set and Decorated Shape Features
Clustering a large number of compounds. 3. The limits of classification
The Most Beautiful Molecule. The Discovery of the Buckyball. By Hugh Aldersey-Williams. John Wiley & Sons: NY 1995, 340 pp. ISBN 0-471-19333-X
Identifying and Characterizing Binding Sites and Assessing Druggability
Combining IC 50 or K i Values from Different Sources Is a Source of Significant Noise
Encoding and Decoding Graphical Chemical Structures as Two-Dimensional (PDF417) Barcodes
Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions
Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes
Evaluation of a Dual Journal Concept
Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity
Long-Time Oxygen Localization in Electron Transfer Flavoprotein
Electronic Laboratory Notebook: The Academic Point of View
A Cellular Automata Model of the Percolation Process
Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm
DARC system for documentation and artificial intelligence in chemistry
Combining Pharmacophore Fingerprints and PLS-Discriminant Analysis for Virtual Screening and SAR Elucidation
Computational Derivation of Structural Alerts from Large Toxicology Data Sets
Contact Parallel Cascade Selection Molecular Dynamics (cPaCS-MD) for Accurate In Silico Prediction of Peptide Binding Free Energy
Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive OR
A Differentiable Neural-Network Force Field for Ionic Liquids
Identification of a Preferred Set of Molecular Descriptors for Compound Classification Based on Principal Component Analysis
Residue Preference Mapping of Ligand Fragments in the Protein Data Bank
Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening
In Silico Calculation of Infinite Dilution Activity Coefficients of Molecular Solutes in Ionic Liquids: Critical Review of Current Methods and New Models Based on Three Machine Learning Algorithms
Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins
Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein-Protein Interface
New Approach by Kriging Models to Problems in QSAR
Nonlinear Partial Least Squares Modeling of Phenyl Alkylamines with the Monoamine Oxidase Inhibitory Activities
Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells
DeepMLP: A Proteomics-Driven Deep Learning Framework for Identifying Mis-Localized Proteins across Pan-Cancer
Application of automated structure analysis to some organic compounds using PCs. 3. Crystallographic programs
Unveiling G-Protein-Coupled Receptor Conformational Dynamics via Metadynamics Simulations and Markov State Models
Finding the Ion in the RNA-Stack: Can Computational Models Accurately Predict Key Functional Elements in Large Macromolecular Complexes?
GB1 Dimerization in Crowders: A Multiple Resolution Approach
Molecular Topographic Indices
Chemical Abstracts as a Patent Reference Tool
Serendipitous Discovery of Short Peptides from Natural Products as Tyrosinase Inhibitors
Is Multitask Deep Learning Practical for Pharma?
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery
KID: A Kinase-Focused Interaction Database and Its Application in the Construction of Kinase-Focused Molecule Databases
Structure-Based Discovery of 1 H -Indazole-3-carboxamides as a Novel Structural Class of Human GSK-3 Inhibitors
Similarity Boosted Quantitative Structure-Activity Relationship - A Systematic Study of Enhancing Structural Descriptors by Molecular Similarity
Automated extraction of spin coupling topologies from 2D NMR correlation spectra for protein proton resonance assignment
Neural Network Based Quantitative Structural Property Relations (QSPRs) for Predicting Boiling Points of Aliphatic Hydrocarbons
List Operations on Chemical Graphs. 5. Implementation of Breadth-First Molecular Path Generation and Application in the Estimation of Retention Index Data and Boiling Points
Novel Approach for the Numerical Characterization of Molecular Chirality
Tuning Stacking Interactions between Asp-Arg Salt Bridges and Heterocyclic Drug Fragments
Topological structural information in the CAS file: statistical occurrences of DARC concentric fragments. 1. Basic carbon substructures
Last Step of the Para Route of the Kolbe-Schmitt Reaction
Understanding Product Specificity of Protein Lysine Methyltransferases from QM/MM Molecular Dynamics and Free Energy Simulations: The Effects of Mutation on SET7/9 beyond the Tyr/Phe Switch
Chemical reaction searching compared in REACCS, SYNLIB, and ORAC
Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein-Peptide Data Set
A Differential-Operator Approach to the Permanental Polynomial
HexagonRingCalculator: A Handy Code for Hexagonal Ring Characterization in Atomistic Simulations
Structure-activity relationship oriented languages for chemical structure representation
Development of an Efficient Geometry Optimization Method for Water Clusters
Why Purine Nucleoside Phosphorylase Ribosylates 2, 6-Diamino-8-azapurine in Noncanonical Positions? A Molecular Modeling Study
Balancing Molecular Size, Activity, Permeability, and Other Properties: Drug Candidates in the Context of Their Chemical Structure Optimization
Theoretical Descriptors for the Correlation of Aquatic Toxicity of Environmental Pollutants by Quantitative Structure-Toxicity Relationships
Transparent Machine Learning Model to Understand Drug Permeability through the Blood-Brain Barrier
Automated Pharmacophore Identification for Large Chemical Data Sets1
Using Neural Network Predicted Secondary Structure Information in Automatic Protein NMR Assignment
A Scaffold-Independent Subcellular Event-Based Analysis: Characterization of Significant Structural Modifications
Optimization of a similarity metric for library searching of highly compressed vapor-phase infrared spectra
An Approach to the Assignment of Canonical Connection Tables and Topological Symmetry Perception
Machine Learning of Analytical Electron Density in Large Molecules Through Message-Passing
Scaffold-Retained Structure Generator to Exhaustively Create Molecules in an Arbitrary Chemical Space
Clustering and Classifying Diverse HIV Entry Inhibitors Using a Novel Consensus Shape-Based Virtual Screening Approach: Further Evidence for Multiple Binding Sites within the CCR5 Extracellular Pocket
T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment
Parametrization Strategy for the MolFESD Concept: Quantitative Surface Representation of Local Hydrophobicity
ColabReaction: Accelerating Transition State Searches with Machine Learning Potentials on Google Colaboratory
Enumeration of Polyene Hydrocarbons: A Complete Mathematical Solution
Learning Coarse-Grained Potentials for Binary Fluids
A Structural Molecular Formula for Flexible and Efficient Substructure Searching of Large Databases
Database Clustering with a Combination of Fingerprint and Maximum Common Substructure Methods
FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations
Improving Spectral Library Search by Redefining Similarity Measures
Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design
Machine-Learning Predictions of Critical Temperatures from Chemical Compositions of Superconductors
Hierarchical PLS Modeling for Predicting the Binding of a Comprehensive Set of Structurally Diverse Protein-Ligand Complexes
Ligand-Based Models for the Isoform Specificity of Cytochrome P450 3A4, 2D6, and 2C9 Substrates
Direct Optimization across Computer-Generated Reaction Networks Balances Materials Use and Feasibility of Synthesis Plans for Molecule Libraries
Cyto-Safe: A Machine Learning Tool for Early Identification of Cytotoxic Compounds in Drug Discovery
Navigating Ultralarge Virtual Chemical Spaces with Product-of-Experts Chemical Language Models
Formulas for the Hyper-Wiener Index of Trees
Could Egg White Lysozyme be Solved by Single Particle Cryo-EM?
PolyConstruct : Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild , PolyConf , and PolyTop
Conformational Plasticity of Interleukin-8 Mediates Its Dynamic Molecular Interaction with Potent Inhibitor Suramin
AIRI: Predicting Retention Indices and Their Uncertainties Using Artificial Intelligence
DeepP450: Predicting Human P450 Activities of Small Molecules by Integrating Pretrained Protein Language Model and Molecular Representation
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes
Synthesis simulation by synthon substitution
Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes
GAPE: An Improved Genetic Algorithm for Pharmacophore Elucidation
Connectionist hyperprism neural network for the analysis of ion mobility spectra: An empirical evaluation
Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain
SMVSNN: An Intelligent Framework for Anticancer Drug-Drug Interaction Prediction Utilizing Spiking Multi-view Siamese Neural Networks
Evaluating Polymer Representations via Quantifying Structure-Property Relationships
Similarity Approach to Chemical Reactivity. Regioselectivity in Pericyclic Reactions
Uncertainty-Informed Screening for Safer Solvents Used in the Synthesis of Perovskites via Language Models
Drug- and Lead-likeness, Target Class, and Molecular Diversity Analysis of 7.9 Million Commercially Available Organic Compounds Provided by 29 Suppliers
Effect of taxonomy class and spanning set on identifying and counting rings in a compound
Exploring Phase-Transfer Catalysis with Molecular Dynamics and 3D/4D Quantitative Structure-Selectivity Relationships
Computational Methods for Predicting Chemical Reactivity of Covalent Compounds
Impact of Native Environment in Multiheme-Cytochrome Chains of the MtrCAB Complex
DARC substructure search system: a new approach to chemical information
Binding Pose Flip Explained via Enthalpic and Entropic Contributions
AIGO-DTI: Predicting Drug-Target Interactions Based on Improved Drug Properties Combined with Adaptive Iterative Algorithms
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans
Polarizability Fields for Use in Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR)
Kinase-Bench: Comprehensive Benchmarking Tools and Guidance for Achieving Selectivity in Kinase Drug Discovery
How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment
Lead Discovery Using Stochastic Cluster Analysis (SCA): A New Method for Clustering Structurally Similar Compounds
Symmetry-Aided Computation of the Detour Matrix and the Detour Index
Reactions in the Beilstein information system: nonaporic organic synthesis
Partitioned-Formula Periodic Tables for Diamond Hydrocarbons (Diamondoids)
Graph-Based Chemical Nomenclature. 2. Incorporation of Graph-Theoretical Principles into Taylor's Nomenclature Proposal
AttMVGraph: Attention-Based Multimodal Fusion and Variational Graph Learning for SM-miRNA Association Prediction
Clustangles: An Open Library for Clustering Angular Data
Artificial Intelligence in Drug Toxicity Prediction: Recent Advances, Challenges, and Future Perspectives
Phosphorylation of Fibronectin Influences the Structural Stability of the Predicted Interchain Domain
Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients
Using AMBER18 for Relative Free Energy Calculations
Copyright: past, present, and future
Evaluating Machine Learning Methods of Analyzing Multiclass Metabolomics
In-Silico Extraction of Design Ideas Using MMPA-by-QSAR and its Application on ADME Endpoints
grand: A Python Module for Grand Canonical Water Sampling in OpenMM
Extended-Connectivity Fingerprints
Genomic Data Analysis Using DNA Structure: An Analysis of Conserved Nongenic Sequences and Ultraconserved Elements
Atomic Shell Approximation: Electron Density Fitting Algorithm Restricting Coefficients to Positive Values
Discovery of Novel Peroxisome Proliferator-Activated Receptor α (PPARα) Agonists by Virtual Screening and Biological Evaluation
Searching for Coordinated Activity Cliffs Using Particle Swarm Optimization
New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability
Three Data Mining Techniques To Improve Lazy Structure-Activity Relationships for Noncongeneric Compounds
The NCI Drug Information System. 3. The DIS chemistry module