yusuke1997/dblp-id-title huggingface dataset:
Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Michael Acceptor Warheads
Generative graphs and representation by induction of orders: the RIO general model of EURECAS
Filling the Gap in Understanding the Mechanism of GABAAR and Propofol Using Computational Approaches
The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data
The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules
B-SIDER: Computational Algorithm for the Design of Complementary β-Sheet Sequences
Meeting the Challenges of the Changing Patent Literature
Atom-by-atom searching using massive parallelism. Implementation of the Ullmann subgraph isomorphism algorithm on the distributed array processor
Cardiotoxins: Functional Role of Local Conformational Changes
Prediction and Experimental Confirmation of Novel Peripheral Cannabinoid-1 Receptor Antagonists
Finding a Kekule Structure in a Benzenoid System in Linear Time
Simulated Drug Efflux for the AbgT Family of Membrane Transporters
The 5-HT 1A Agonism Potential of Substituted Piperazine-Ethyl-Amide Derivatives Is Conserved in the Hexyl Homologues: Molecular Modeling and Pharmacological Evaluation
Reaction Graphs for Square Antiprism Rearrangements
LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design
Evaluation of Virtual Screening Performance of Support Vector Machines Trained by Sparsely Distributed Active Compounds
Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac Myosin
Conformal Selection for Efficient and Accurate Compound Screening in Drug Discovery
Upper and lower bounds for molecular energies
ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors
Experimentally Validated hERG Pharmacophore Models as Cardiotoxicity Prediction Tools
Exposing the Limitations of Molecular Machine Learning with Activity Cliffs
Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O -Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses
Intuitive Ordering of Scaffolds and Scaffold Similarity Searching Using Scaffold Keys
AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: From the c-Kit Proto-Oncogene to HIV-1
Virtual Screening of Hole Transport, Electron Transport, and Host Layers for Effective OLED Design
International recommendations for handling copyright questions about computer-generated works: what are our concerns?
Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 3. Hierarchical Model of Screening of Chemical Databases
Virtual Exploration of the Ring Systems Chemical Universe
Pharmacophore Modeling as an Efficient Tool in the Discovery of Novel Noncompetitive AMPA Receptor Antagonists
SynthI: A New Open-Source Tool for Synthon-Based Library Design
Does Rational Selection of Training and Test Sets Improve the Outcome of QSAR Modeling?
Development of Linear, Ensemble, and Nonlinear Models for the Prediction and Interpretation of the Biological Activity of a Set of PDGFR Inhibitors
Structural Chemistry of the Histone Methyltransferases Cofactor Binding Site
Development of Machine Learning Models and the Discovery of a New Antiviral Compound against Yellow Fever Virus
Topological organic chemistry. 6. Graph theory and molecular topological indexes of cycloalkanes
A Universal Molecular Descriptor System for Prediction of LogP, LogS, LogBB, and Absorption
Critical Point Representations of Electron Density Maps for the Comparison of Benzodiazepine-Type Ligands
Shape and Size of Giant Unilamellar Phospholipid Vesicles Containing Cardiolipin
Prediction of Physicochemical Parameters by Atomic Contributions
Flexibility and Hydration of the Q o Site Determine Multiple Pathways for Proton Transfer in Cytochrome bc 1
Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions
Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 2. Application to Clustering of Chemical Databases
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing
Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors
Protein Pharmacophore Selection Using Hydration-Site Analysis
Development of Reliable Aqueous Solubility Models and Their Application in Druglike Analysis
Prediction of Methyl Radical Addition Rate Constants from Molecular Structure
Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs
Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States
Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation
Allowed Boundary Sequences for Fused Polycyclic Patches and Related Algorithmic Problems
FLUFF-BALL, A Template-Based Grid-Independent Superposition and QSAR Technique: Validation Using a Benchmark Steroid Data Set
How Important Is the Synclinal Conformation of Sulfonylureas To Explain the Inhibition of AHAS: A Theoretical Study
Parameterization of General Organic Polymers within the Open Force Field Framework
Isomer Generation: Syntactic Rules for Detection of Isomorphism
Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing"
Insights into AT 1 Receptor Activation through AngII Binding Studies
Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise
Definition of Drug-Likeness for Compound Affinity
Understanding the Structure-Function Relationship of Lysozyme Resistance in Staphylococcus aureus by Peptidoglycan O-Acetylation Using Molecular Docking, Dynamics, and Lysis Assay
A Cellular Automata Model of Acid Dissociation
Using Domain-Specific Fingerprints Generated Through Neural Networks to Enhance Ligand-Based Virtual Screening
A Dominant Factor for Structural Classification of Protein Crystals
Optimizing Vanadium-Catalyzed Epoxidation Reactions: Machine-Learning-Driven Yield Predictions and Data Augmentation
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity
MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations
Probing the Structural Dynamics of the Unbound MAX Protein: Insights from Well-Tempered Metadynamics
Pocketome of Human Kinases: Prioritizing the ATP Binding Sites of (Yet) Untapped Protein Kinases for Drug Discovery
Topological organic chemistry. 1. Graph theory and topological indices of alkanes
Rigorous Computational Study Reveals What Docking Overlooks: Double Trouble from Membrane Association in Protein Kinase C Modulators
Practical Outcomes of Applying Ensemble Machine Learning Classifiers to High-Throughput Screening (HTS) Data Analysis and Screening
Differential Effects of IL2Rα and IL15Rα over the Stability of the Common Beta-Gamma Signaling Subunits of the IL2 and IL15 Receptors
Exhaustive generation of organic isomers. 1. Acyclic structures
Factors involved in Japan's contribution to international chemical information activities: present status and prospects
PyBindingCurve, Simulation, and Curve Fitting to Complex Binding Systems at Equilibrium
Classification of Some Active Compounds and Their Inactive Analogues Using Two Three-Dimensional Molecular Descriptors Derived from Computation of Three-Dimensional Convex Hulls for Structures Theoretically Generated for Them
Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening
Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4
A General Treatment of Solubility. 1. The QSPR Correlation of Solvation Free Energies of Single Solutes in Series of Solvents
Quantitative Kinetic Model of CO2 Absorption in Aqueous Tertiary Amine Solvents
Activation Mechanism of Strigolactone Receptors and Its Impact on Ligand Selectivity between Host and Parasitic Plants
Universal Organic Solvent-Water Partition Coefficient Model
Chem-X and CAMBRIDGE. Comparison of computer generated chemical structures with x-ray crystallographic data
Molecular Dynamics Simulations of the Ligand-Induced Chemical Information Transfer in the 5-HT 1A Receptor
Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs
Mechanism of Regio- and Enantioselective Hydroxylation of Arachidonic Acid Catalyzed by Human CYP2E1: A Combined Molecular Dynamics and Quantum Mechanics/Molecular Mechanics Study
The knowledge-based organic physical property data system (KB-OPDS)
Freely Available Conformer Generation Methods: How Good Are They?
Combinatorial QSAR of Ambergris Fragrance Compounds
Conformational Sampling of Bioactive Molecules: A Comparative Study
A DNA Algorithm for the Graph Coloring Problem
Building a Chemical Ingredient Data Base for Industrial and Consumer Products
Subpocket Analysis Method for Fragment-Based Drug Discovery
Automated Identification of Chemical Series: Classifying like a Medicinal Chemist
Leveraging Protein Dynamics to Identify Functional Phosphorylation Sites using Deep Learning Models
Evaluation of Mutual Information and Genetic Programming for Feature Selection in QSAR
Construction of the Veterinary DrugBank and Drug Repurposing
In Silico Exploration of Conformational Dynamics and Novel Inhibitors for Targeting MEF2-Associated Transcriptional Activity
miPEPPred-FRL: A Novel Method for Predicting Plant MiRNA-Encoded Peptides Using Adaptive Feature Representation Learning
Empirical stability rules and conjugation in the estimation of enthalpies of formation
Structural Properties of Non-Traditional Drug Targets Present New Challenges for Virtual Screening
CoNSEnsX + Webserver for the Analysis of Protein Structural Ensembles Reflecting Experimentally Determined Internal Dynamics
Virtual Screening of Novel and Selective Inhibitors of Protein Tyrosine Phosphatase 1B over T-Cell Protein Tyrosine Phosphatase Using a Bidentate Inhibition Strategy
Modeling MEK4 Kinase Inhibitors through Perturbed Electrostatic Potential Charges
Mechanistic Reactivity Descriptors for the Prediction of Ames Mutagenicity of Primary Aromatic Amines
Economical and Accurate Protocol for Calculating Hydrogen-Bond-Acceptor Strengths
Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach
A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters
In silico Prediction of Chemical Ames Mutagenicity
Computer-Assisted Synthetic Analysis. Long-Range Search Procedures for Antithetic Simplification of Complex Targets by Application of the Halolactonization Transform
Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides
Development of Quantitative Structure-Property Relationships Using Calculated Descriptors for the Prediction of the Physicochemical Properties (nD, , bp, , ) of a Series of Organic Solvents
Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics
How the WLN began in 1949 and how it might be in 1999
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance
SF-Rx: A Multioutput Deep Neural Network-Based Framework Predicting Drug-Drug Interaction under Realistic Conditions for Safe Prescription
Dollars-and-cents value of efficient presentation. A plea for the retention of the well-produced primary journal
Prediction of Retention Time and Collision Cross Section (CCS H+ , CCS H- , and CCS Na+ ) of Emerging Contaminants Using Multiple Adaptive Regression Splines
Role of Aromacity, Ring Strain, and Stereochemistry of Selected Disulfides and Their Congeners in the Oxidative Linkage of DNA Strands at the Major Groove. A Computational Study
Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase
Large Data Base at the Lawrence Livermore Laboratory
Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations
Learning from the Data: Mining of Large High-Throughput Screening Databases
Question of data format in organic chemistry
Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways
Nontraditional Careers for Chemists: New Formulas in Chemistry By Lisa M. Balbes. Oxford University Press, New York, NY, 2007. xi + 307 pp + bibliography and indexes. ISBN 0-19-518366-5, hardcover, U.S. $74.50. ISBN 0-19-518367-3, softcover, U.S. $27.95
Transformer Decoder Learns from a Pretrained Protein Language Model to Generate Ligands with High Affinity
Combining a Chemical Language Model and the Structure-Activity Relationship Matrix Formalism for Generative Design of Potent Compounds with Core Structure and Substituent Modifications
Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds
Unraveling the Allosteric Cross-Talk between the Coactivator Peptide and the Ligand-Binding Site in the Glucocorticoid Receptor
Predicting Class I Major Histocompatibility Complex (MHC) Binders Using Multivariate Statistics: Comparison of Discriminant Analysis and Multiple Linear Regression
Comparative Analysis of Pharmacophore Screening Tools
Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function
No Electron Left Behind: A Rule-Based Expert System To Predict Chemical Reactions and Reaction Mechanisms
Comparison of manual and online searches of Chemical Abstracts
How Does the Quality of Phospholipidosis Data Influence the Predictivity of Structural Alerts?
Differential Shannon Entropy Analysis Identifies Molecular Property Descriptors that Predict Aqueous Solubility of Synthetic Compounds with High Accuracy in Binary QSAR Calculations
DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space
Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark
Theoretical Analysis of Selectivity Differences in Ketoreductases toward Aldehyde and Ketone Carbonyl Groups
Novel Kinase Inhibitors by Reshuffling Ligand Functionalities Across the Human Kinome
General Combinatorics of RNA Hairpins and Cloverleaves
Linear and Nonlinear Procedures in Isoconversional Computations of the Activation Energy of Nonisothermal Reactions in Solids
Exploring the Role of Water Molecules for Docking and Receptor Guided 3D-QSAR Analysis of Naphthyridine Derivatives as Spleen Tyrosine Kinase (Syk) Inhibitors
Iterated similarity sequences and shape ID numbers for molecules
Atomic Decomposition Scheme of Noncovalent Interactions Applied to Host-Guest Assemblies
Study on structure-activity relationships of organic compounds: Three new topological indexes and their applications
Enhanced Polymer Structure, Searching, and Retrieval in an Interactive Database
Nonparametric Regression Applied to Quantitative Structure-Activity Relationships
Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA)
VADER: New Software for Exploring Interconversions on Potential Energy Surfaces
Large-Scale Modeling of Sparse Protein Kinase Activity Data
Binding Models of Aβ42 Peptide with Membranes Explored by Molecular Simulations
Structural and Computational Insights into the Mechanism of the Superior Pharmacological Activity of Crisugabalin: A Third-Generation Cavα 2 δ1 Ligand
Semisupervised Contrastive Learning for Bioactivity Prediction Using Cell Painting Image Data
ReactionDataExtractor: A Tool for Automated Extraction of Information from Chemical Reaction Schemes
Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity
Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease
Representing Catalytic Mechanisms with Rule Composition
Role of Wave Functions' Nodal Surfaces in Interpretation of the Pauli Principle
Computerized retrieval of information on biosynthesis and metabolic pathways
Identification and Validation of Novel PERK Inhibitors
Isomer Generation: Semantic Rules for Detection of Isomorphism
Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution
FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists
gNMR version 3 for Macintosh
A DIRECT-SEARCHER Automatic System (Version 3) for Some Organic Compounds Running on Personal Computers
Energy-Based Pharmacophore and Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) Modeling Combined with Virtual Screening To Identify Novel Small-Molecule Inhibitors of Silent Mating-Type Information Regulation 2 Homologue 1 (SIRT1)
Reaction between Ellagic Acid and an Ultimate Carcinogen
Prediction of Drug Solubility by the General Solubility Equation (GSE)
DStruBTarget: Integrating Binding Affinity with Structure Similarity for Ligand-Binding Protein Prediction
Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design
Drug Effect Prediction by Polypharmacology-Based Interaction Profiling
Phytochemical Databases of Chinese Herbal Constituents and Bioactive Plant Compounds with Known Target Specificities
Maximum-Score Diversity Selection for Early Drug Discovery
Prediction of Complement-Inhibitory Activity of Benzamidines Using Topological and Geometric Parameters
DO-GMA: An End-to-End Drug-Target Interaction Identification Framework with a Depthwise Overparameterized Convolutional Network and the Gated Multihead Attention Mechanism
Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations
FragOPT: An ML-Driven Computational Workflow for Rational Fragments Optimization Toward Lead Compounds
MILCDock: Machine Learning Enhanced Consensus Docking for Virtual Screening in Drug Discovery
Structure and Properties of the Nonface-Spiral Fullerenes T -C 380 , D 3 -C 384 , D 3 -C 440 , and D 3 -C 672 and Their Halma and Leapfrog Transforms
Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution
A Quantum and Deductive Chemical Study for All Congeners of Polybromo/Chlorodibenzo- p- dioxin and Polybromo/Chlorodibenzofuran
Enhanced algorithm for finding the smallest set of smallest rings
NLM-CHEMSORT: an algorithm and computer program for sorting chemical names
Expansion of Matula Numbers to Heteroatoms and to Ring Compounds
A Comparison of the Performance of Some Similarity and Dissimilarity Measures in the Automatic Classification of Chemical Structures
Concept-Based Semi-Automatic Classification of Drugs
Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide
Fragment Linker Prediction Using the Deep Encoder-Decoder Network for PROTACs Drug Design
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations
The Publication Speed of Information in Bibliographic Chemical Databases
Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms
Beware of Unreliable Q 2 ! A Comparative Study of Regression Metrics for Predictivity Assessment of QSAR Models
The walk ID number revisited. [Erratum to document cited in CA118: 146918]
A Quick, Systematic Method for Worldwide Patent Awareness
The E-State as the Basis for Molecular Structure Space Definition and Structure Similarity
Reconstruction of the Fas-Based Death-Inducing Signaling Complex (DISC) Using a Protein-Protein Docking Meta-Approach
CerBeruS: A System Supporting the Sequential Screening Process
Vina-GPU 2.0: Further Accelerating AutoDock Vina and Its Derivatives with Graphics Processing Units
Infrared Spectral Analysis for Prediction of Functional Groups Based on Feature-Aggregated Deep Learning
A New Fingerprint and Graph Hybrid Neural Network for Predicting Molecular Properties
Ligand-Based Virtual Screening by Novelty Detection with Self-Organizing Maps
Has Nomenclature Gone to Pot?
Correction to "Unraveling the Abnormal Molecular Mechanism of Suicide Inhibition of Cytochrome P450 3A4"
Machine Learning-Enabled Pipeline for Large-Scale Virtual Drug Screening
The Effectiveness of Reactant Pools for Generating Structurally-Diverse Combinatorial Libraries
Molecular Dynamics Simulations of the Interaction of Beta Cyclodextrin with a Lipid Bilayer
Water Network-Augmented Two-State Model for Protein-Ligand Binding Affinity Prediction
Evaluation of Interactions between SARS-CoV-2 RBD and Full-Length ACE2 with Coarse-Grained Molecular Dynamics Simulations
Lead Validation and SAR Development via Chemical Similarity Searching; Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56 lck
Computers in the new drug application process
The "Carpet-like" Mechanism of NaD1 on Candida albicans Cell Membranes at Low NaD1/Lipid Ratios Revealed by Molecular Dynamics Simulations
Exploration of Rate-Limiting Conformational State for 5-[(7-Chloro-4-quinolinyl)amino]-3-[(alkylamino)methyl][1, 1'-biphenyl]-2-ols and N ω -Oxides (Tebuquine Analogues) for Antimalarial Activity Using Molecular Shape Analysis and Molecular Field Analysis Studies
The Effect of Debiasing Protein-Ligand Binding Data on Generalization
Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design
A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes
Prediction of Active Site Cleft Using Support Vector Machines
AutoDesigner, a De Novo Design Algorithm for Rapidly Exploring Large Chemical Space for Lead Optimization: Application to the Design and Synthesis of d-Amino Acid Oxidase Inhibitors
Using Artificial Neural Networks To Classify the Activity of Capsaicin and Its Analogues
Homology Model-Guided 3D-QSAR Studies of HIV-1 Integrase Inhibitors
Exploration of a Binding Mode of Benzothiazol-2-yl Acetonitrile Pyrimidine Core Based Derivatives as Potent c-Jun N-Terminal Kinase-3 Inhibitors and 3D-QSAR Analyses
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate
An Open-Source Java Platform for Automated Reaction Mapping
Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3
Computational Saturation Screen Reveals the Landscape of Mutations in Human Fumarate Hydratase
Exhaustive generation of organic isomers. 2. Cyclic structures: new compact molecular code
Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics
Computer-assisted topological analysis and completion of chemical reactions
AUTOSURF: A Freely Available Program To Construct Potential Energy Surfaces
Modeling Reactions from Chemical Theories to Machine Learning
The Trouble with QSAR (or How I Learned To Stop Worrying and Embrace Fallacy)
A Coarse-Grained Molecular Dynamics Approach to the Study of the Intrinsically Disordered Protein α-Synuclein
JACOB: A Dynamic Database for Computational Chemistry Benchmarking
Identification of a Potential Zika Virus Inhibitor Targeting NS5 Methyltransferase Using Virtual Screening and Molecular Dynamics Simulations
Chirality Codes and Molecular Structure
Chemically Informed Deep Learning for Interpretable Radical Reaction Prediction
Using Three-Dimensional Information to Predict and Interpret the Facial Selectivities of Nucleophilic Additions to Cyclic Ketones
An Algorithm for the Perception of Synthetically Important Rings