yusuke1997/dblp-id-title huggingface dataset:
A method for automatic generation of novel chemical structures and its potential applications to drug discovery
Predict Ionization Energy of Molecules Using Conventional and Graph-Based Machine Learning Models
Template-Based Method for Conformation Generation and Scoring for Congeneric Series of Ligands
FunQG: Molecular Representation Learning via Quotient Graphs
The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions
Importance of Three-Body Problems and Protein-Protein Interactions in Proteolysis-Targeting Chimera Modeling: Insights from Molecular Dynamics Simulations
Applying Medicinal Chemistry Transformations and Multiparameter Optimization to Guide the Search for High-Quality Leads and Candidates
Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites
Allosteric Boost by TAB1 on the TAK1 Kinase Favorably Sculpts the Thermodynamic Landscape of Activation
A Molecular Dynamics Investigation of the Thermostability of Cold-Sensitive I707L KlenTaq1 DNA Polymerase and Its Wild-Type Counterpart
Retrieval and interpretative computer programs for mass spectrometry
Comprehensive 3D-QSAR Model Predicts Binding Affinity of Structurally Diverse Sigma 1 Receptor Ligands
Automorphism and equivalence classes
SkeleDock: A Web Application for Scaffold Docking in PlayMolecule
Message Passing Neural Networks Improve Prediction of Metabolite Authenticity
Semi-supervised Hierarchical Drug Embedding in Hyperbolic Space
Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine
Diagnostic Tools to Determine the Quality of "Transparent" Regression-Based QSARs: The "Modelling Power" Plot
MS-WHIM Scores for Amino Acids: A New 3D-Description for Peptide QSAR and QSPR Studies
Multiple Structures for Virtual Ligand Screening: Defining Binding Site Properties-Based Criteria to Optimize the Selection of the Query
Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with e MolFrag
Universal J -Coupling Prediction
VeGA: A Versatile Generative Architecture for Bioactive Molecules across Multiple Therapeutic Targets
Graphic Representation of Configuration in Two-Dimensional Space. Current Conventions, Clarifications, and Proposed Extensions1, 2
In Silico Binding Free Energy Predictability by Using the Linear Interaction Energy (LIE) Method: Bromobenzimidazole CK2 Inhibitors as a Case Study
A Computational Approach To Design and Evaluate Enzymatic Reaction Pathways: Application to 1-Butanol Production from Pyruvate
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels
Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth
Modeling the Solvation Sites in Rare-Gas Matrices with the Simulated Annealing Monte Carlo Technique
Efficient Heuristics for Maximum Common Substructure Search
BrainPepPass: A Framework Based on Supervised Dimensionality Reduction for Predicting Blood-Brain Barrier-Penetrating Peptides
PULSAR: a personalized microcomputer-based system for keyword search and retrieval of literature information
A Hierarchical Clustering Approach for Large Compound Libraries
Molecular Gas-Phase Conformational Ensembles
Quantum Mechanical/Molecular Mechanical Study of Catalytic Mechanism and Role of Key Residues in Methylation Reactions Catalyzed by Dimethylxanthine Methyltransferase in Caffeine Biosynthesis
Exploration of Interfacial Hydration Networks of Target-Ligand Complexes
Computer Control of Data Acquisition, Reduction, and Display in Rapid Scanning Liquid Chromatography
Path-Integral Calculation of the Mean Number of Overcrossings in an Entangled Polymer Network
Studies on the Metallurgical Patent Literature. I. The Coverage of Patents by Abstracts Journals in Metallurgy
Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained on Docked Poses
Neighborhood Behavior of in Silico Structural Spaces with Respect to In Vitro Activity Spaces-A Benchmark for Neighborhood Behavior Assessment of Different in Silico Similarity Metrics
Misfolding and Self-Assembly Dynamics of Microtubule-Binding Repeats of the Alzheimer-Related Protein Tau
Comparison of Computational Methods to Model DNA Minor Groove Binders
Decisions with Confidence: Application to the Conformation Sampling of Molecules in the Solid State
The standard molecular data format (SMD format) as an integration tool in computer chemistry
Deep Generative Models for 3D Linker Design
Enumeration of Polyhex Hydrocarbons to h = 17
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction
Expert System for Predicting Reaction Conditions: The Michael Reaction Case
Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis
ALF-A: a knowledge acquisition tool for troubleshooting of laboratory equipment
Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations
Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing
Design of an Expert System for Emergency Response to a Chemical Spill, 1. Domain Definition and Knowledge Acquisition
Chemical Proteomic Tool for Ligand Mapping of CYP Antitargets: An NMR-Compatible 3D QSAR Descriptor in the Heme-Based Coordinate System
RASA: A Rapid Retrosynthesis-Based Scoring Method for the Assessment of Synthetic Accessibility of Drug-like Molecules
Precedent Finder: Locating Pareto-Optimal Reactions
SynKit : A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis
StemCellCKB: An Integrated Stem Cell-Specific Chemogenomics KnowledgeBase for Target Identification and Systems-Pharmacology Research
BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical Space
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank
Structural Insight into the Inactive/Active States of 5-HT1AR and Molecular Mechanisms of Electric Fields in Modulating 5-HT1AR
Fast and Reliable Thermodynamic Approach for Determining the Protonation State of the Asp Dyad
Predicting Total Clearance in Humans from Chemical Structure
Building a Three-Dimensional Model of CYP2C9 Inhibition Using the Autocorrelator: An Autonomous Model Generator
Using Random Forest To Model the Domain Applicability of Another Random Forest Model
Final Cut Express HD: Digital Video Editing for Everyone (Apple Pro Training) By Diana Weynand. Adobe (Peachpit) Press: Berkeley, CA, 2006, 512 pp and DVD. ISBN 0-321-33533-3. Softcover. U.S. $49.99
Novel Receptor Surface Approach for 3D-QSAR: The Weighted Probe Interaction Energy Method
Cavities Tell More than Sequences: Exploring Functional Relationships of Proteases via Binding Pockets
Interpretable Deep-Learning p K a Prediction for Small Molecule Drugs via Atomic Sensitivity Analysis
Monitoring the Quality of a Chemical Production Process Using the Joint Estimation Method
Integrated chemical-biological-spectroscopy-inventory-reactions preclinical database
Structure-Based Approach for the Study of Estrogen Receptor Binding Affinity and Subtype Selectivity
Structure Elucidator: A Versatile Expert System for Molecular Structure Elucidation from 1D and 2D NMR Data and Molecular Fragments
Extensive Assessment of Various Computational Methods for Aspartate's p K a Shift
Exploring the Intrinsic Structural Plasticity and Conformational Dynamics of Human Beta Coronavirus Spike Glycoproteins
Complexity of Molecules
Antihypertensive Drug Valsartan in Solution and at the AT 1 Receptor: Conformational Analysis, Dynamic NMR Spectroscopy, in Silico Docking, and Molecular Dynamics Simulations
Dimeric Hold States of Anti-HIV Protein SAMHD1 are Redox Tunable
Targeting the BH3 Domain Mediated Protein-Protein Interaction of Bcl-xL through Virtual Screening
Mechanistic Aspects of Propene Epoxidation by Hydrogen Peroxide. Catalytic Role of Water Molecules, External Electric Field, and Zeolite Framework of TS-1
How To Add Chemical Abstracts Service Registry Numbers and Structures to Databases via Chemical Names Comparison
Fourier transform infrared spectroscopy without an FTIR spectrometer: library searching and concise storage of spectra
Some heuristics for nearest-neighbor searching in chemical structure files
Polymers and Patents Don't Mix-Easily
Ligand-Based Drug Discovery Leveraging State-of-the-Art Machine Learning Methodologies Exemplified by Cdr1 Inhibitor Prediction
Resolution of ambiguities in structure-property studies by use of orthogonal descriptors
Edge-Connectivity Indices in QSPR/QSAR Studies, 1. Comparison to Other Topological Indices in QSPR Studies
Discovery of Novel SIRT1/2 Inhibitors with Effective Cytotoxicity against Human Leukemia Cells
Deterministic control in knowledge-based systems: application to the development of a cybernetic analytical instrument
Heuristic approaches to the design of a cybernetic electroanalytical instrument
Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy
Introduction of two-dimensional NMR spectral information to an automated structure elucidation system, CHEMICS. Utilization of 2D-INADEQUATE information
Pharmacophore Assessment Through 3-D QSAR: Evaluation of the Predictive Ability on New Derivatives by the Application on a Series of Antitubercular Agents
Evaluation of p K a Estimation Methods on 211 Druglike Compounds
NAOMI nova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures
Computer-assisted studies of molecular structure biological activity relationships
The Scope of Structural Isomerism
Heteroaromatic π-Stacking Energy Landscapes
Profile-QSAR and Surrogate AutoShim Protein-Family Modeling of Proteases
13C NMR Chemical Shift Prediction of the sp3 Carbon Atoms in the Position Relative to the Double Bond in Acyclic Alkenes
Stigmata: An Algorithm To Determine Structural Commonalities in Diverse Datasets
Chemical Library Subset Selection Algorithms: A Unified Derivation Using Spatial Statistics
Cationic polyene cyclizations. A computer assisted synthesis approach
Application of the Novel Molecular Alignment Method Using the Hopfield Neural Network to 3D-QSAR
DAKB-GPCRs: An Integrated Computational Platform for Drug Abuse Related GPCRs
The Information Revolution: Impact on Science and Technology. Edited by J.-E. Dubois and N. Gershon. Springer: Berlin, 1996, 273 pp, ISBN: 3-540-60855-9
Predicting Oral Druglikeness by Iterative Stochastic Elimination
Targeting SARS-CoV-2 Receptor Binding Domain and Main Protease with D-Peptides
EDWARD: E(3)-Equivariant Dual-Way Attentive Reduction for Peptide-to-Small-Molecule Design
A Readable Chemical Notation
Predicting Oxidation Potentials with DFT-Driven Machine Learning
Global and Local Computational Models for Aqueous Solubility Prediction of Drug-Like Molecules
Principles of the Generation of Constitutional and Configurational Isomers
Benchmarking 2D/3D/MD-QSAR Models for Imatinib Derivatives: How Far Can We Predict?
A Bayesian Optimization-Based Hybrid Deep Prediction Method for Zinc-Binding Protein Interaction Sites
OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order-n Algorithm in LAMMPS
Neural Network Prediction of the Solvatochromic Polarity/Polarizability Parameter Pi H 2 [S_EL2;quad]
Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics
Application of Tolerances, Standards, and Methodology in the Enforcement of the Food, Drug, and Cosmetic Act
Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors
Description of organic reactions based on imaginary transition structures. 6. Classification and enumeration of two-string reactions with one common node
Investigation of a Data Split Strategy Involving the Time Axis in Adverse Event Prediction Using Machine Learning
Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening
A New Algorithm for Exhaustive Ring Perception in a Molecular Graph
Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model
Evaluation of Level Pattern Indices
AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro
NPCoronaPredict: A Computational Pipeline for the Prediction of the Nanoparticle-Biomolecule Corona
Interactive Pattern Recognition in the Chemical Laboratory
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials
Ensemble-Based Thermodynamics of the Fuzzy Binding between Intrinsically Disordered Proteins and Small-Molecule Ligands
Structure to Property: Chemical Element Embeddings for Predicting Electronic Properties of Crystals
Quantitative Prediction of log k of Peptides in High-Performance Liquid Chromatography Based on Molecular Descriptors by Using the Heuristic Method and Support Vector Machine
Algorithms for Unique and Unambiguous Coding and Symmetry Perception of Molecular Structure Diagram. III. Method of Subregion Analysis for Unique Coding and Symmetry Perception
Spectrum comparison of IR data taken from different spectrometers with various precision
Investigation of Unprecedented Sites and Proposition of New Ligands for Programmed Cell Death Protein I through Molecular Dynamics with Probes and Virtual Screening
Modeling Complex Metabolic Reactions, Ecological Systems, and Financial and Legal Networks with MIANN Models Based on Markov-Wiener Node Descriptors
Rapid Scanning Structure-Activity Relationships in Combinatorial Data Sets: Identification of Activity Switches
T3 scientific word processing system
Identification of the Druggable Concavity in Homology Models Using the PLB Index
Automatic Prediction of Band Gaps of Inorganic Materials Using a Gradient Boosted and Statistical Feature Selection Workflow
Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho
Model Reduction in the Computational Modeling of Reaction Systems
FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes
Some Problems Encountered in Interdisciplinary Searches of the Polymer Literature
A Probabilistic Approach to Classifying Metabolic Stability
Structure-Aware Heterogeneous Information Fusion Framework for Protein-Ligand Binding Affinity Prediction
Structure-Based Multiscale Approach for Identification of Interaction Partners of PDZ Domains
An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy
Alkane/Water Partition Coefficient Calculation Based on the Modified AM1 Method and Internal Hydrogen Bonding Sampling Using COSMO-RS
Nodeless Valence (Pseudo)spinors
Novel Consensus Docking Strategy to Improve Ligand Pose Prediction
How H-Bonding Affects Aromaticity of the Ring in Variously Substituted Phenol Complexes with Bases. 4. Molecular Geometry as a Source of Chemical Information
Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity
Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines
Puckering Coordinates of Monocyclic Rings by Triangular Decomposition
Flexible Web Service Infrastructure for the Development and Deployment of Predictive Models
Symmetric Structures in the Universe of Protein Folds
Spin Label EPR-Based Characterization of Biosystem Complexity
NRIMD, a Web Server for Analyzing Protein Allosteric Interactions Based on Molecular Dynamics Simulation
D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics
Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond
Molecular Dynamics Approach to Probe the Allosteric Inhibition of PTP1B by Chlorogenic and Cichoric Acid
SchNet_IIA: Potential Energy Surface Fitting by Interatomic Interactions Attention Based on Transfer Learning Analysis
Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum
New and Original p K a Prediction Method Using Grid Molecular Interaction Fields
Monovalent Ionic Atmosphere Modulates the Selection of Suboptimal RNA Sequences by Splicing Factors' RNA Recognition Motifs
Chemical Name to Structure: OPSIN, an Open Source Solution
The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant
Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark
Bayesian Model Based Clustering Analysis: Application to a Molecular Dynamics Trajectory of the HIV-1 Integrase Catalytic Core
"The Merck Index": The Merits of Using Computers in Publishing
On Molecular Polarizability: 3. Relationship to the Ionization Potential of Haloalkanes, Amines, Alcohols, and Ethers
Symposium on User Reactions to CAS Data and Bibliographic Services. Concluding Remarks
Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data
Analytical Estimation of Scaling Behavior for the Entanglement Complexity of a Bond Network
Managing the Computational Chemistry Big Data Problem: The ioChem-BD Platform
Cost effectiveness of on-line searching of chemical information: an industrial viewpoint
A Linear Algorithm for the Hyper-Wiener Index of Chemical Trees
CLIP: Similarity Searching of 3D Databases Using Clique Detection
Virtual Drug Screen Schema Based on Multiview Similarity Integration and Ranking Aggregation
Transferable Ring Corrections for Predicting Enthalpy of Formation of Cyclic Compounds
Named Organic Reactions By Thomas Laue and Andreas Plagens. John Wiley & Sons: Chichester, UK, 1998, 288 pp. ISBN 0-471-97142-1
ESIgen: Electronic Supporting Information Generator for Computational Chemistry Publications
Effects of Defects and Presence of Open-Metal Sites on the Structure and Dynamics of Water in Hydrophobic Zeolitic Imidazolate Frameworks
Molecular Insights on the Conformational Transitions and Activity Regulation of the c-Met Kinase Induced by Ligand Binding
Insight into Antioxidant and Photoprotective Properties of Natural Compounds from Marine Fungus
Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields
Applications of degree distribution. 1. (a) General discussion and computer generation of degree distributions. (b) Maximal degree distributions
Assessing Model Fit by Cross-Validation
Protein Surface Printer for Exploring Protein Domains
Protein Design Based on Parallel Dimensional Reduction
Assessing the Performance of the Nonbonded Mg2+ Models in a Two-Metal-Dependent Ribonuclease
MonteCat: A Basin-Hopping-Inspired Catalyst Descriptor Search Algorithm for Machine Learning Models
Informatics for Chemistry, Biology, and Biomedical Sciences
Benchmarking Methods for PROTAC Ternary Complex Structure Prediction
Chemical Manufacturers Electronic Directory of Trade Name Products 1997 Edition on CD-ROM
Conformational Analysis of 6α- and 6β-Naltrexol and Derivatives and Relationship to Opioid Receptor Affinity
Developing a User-Friendly Code for the Fast Estimation of Well-Behaved Real-Space Partial Charges
A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry
A Machine Learning Model for the Proteome-Wide Prediction of Lipid-Interacting Proteins
Structural Basis of Specific Binding between Aurora A and TPX2 by Molecular Dynamics Simulations
Molecular Docking of Cathepsin L Inhibitors in the Binding Site of Papain
Drug-Target Interactions Prediction at Scale: The Komet Algorithm with the LCIdb Dataset
QSAR Study of Steroid Benchmark and Dipeptides Based on MEDV-13
Predicting the Brain-To-Plasma Unbound Partition Coefficient of Compounds via Formula-Guided Network
Rationalizing Predictions of Isoform-Selective Phosphoinositide 3-Kinase Inhibitors Using MolAnchor Analysis
Benchmarking Molecular Feature Attribution Methods with Activity Cliffs
Computerized extrapolation of hydrolysis rate data
A Comparative Study of Marginalized Graph Kernel and Message-Passing Neural Network
HiREX: High-Throughput Reactivity Exploration for Extended Databases of Transition-Metal Catalysts
Analysis of Data Fusion Methods in Virtual Screening: Theoretical Model
ChemOffice Ultra 7.0
Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment
Evolving Interpretable Structure-Activity Relationship Models. 2. Using Multiobjective Optimization To Derive Multiple Models
Relative Atomic Moments as Squared Principal Eigenvector Coefficients
Active Library on Corrosion 2.0
Quantum Mechanical Energy-Based Screening of Combinatorially Generated Library of Tautomers. TauTGen: A Tautomer Generator Program
Large-Scale Annotation of Small-Molecule Libraries Using Public Databases
Drugs and Nondrugs: An Effective Discrimination with Topological Methods and Artificial Neural Networks
Computer storage and retrieval of generic chemical structures in patents, 1. Introduction and general strategy
Accuracy Assessment and Automation of Free Energy Calculations for Drug Design
Correction for Electronic Structure Investigation and Parametrization of Biologically Relevant Iron-Sulfur Clusters
Synthesis, Molecular Docking, Molecular Dynamics Studies, and Biological Evaluation of 4 H -Chromone-1,2,3,4-tetrahydropyrimidine-5-carboxylate Derivatives as Potential Antileukemic Agents
In Silico Prediction of Chemical Acute Oral Toxicity Using Multi-Classification Methods
Disconnected Maximum Common Substructures under Constraints
Identification of .beta.-sheet motifs, of .psi.-loops, and of patterns of amino acid residues in three-dimensional protein structures using a subgraph-isomorphism algorithm
Protein Engineering with Lightweight Graph Denoising Neural Networks
Integrated Approach Including Docking, MD Simulations, and Network Analysis Highlights the Action Mechanism of the Cardiac hERG Activator RPR260243
Topological indices and real number vertex invariants based on graph eigenvalues or eigenvectors
HetGAT-LMI: Interpretable Heterogeneous Graph Attention Method for Predicting lncRNA-miRNA Interactions
Infrared Spectrum of 4-Methoxypicolinic Acid N -Oxide: Computation of Asymmetric O-H Stretching Band
Model-Free Drug-Likeness from Fragments
Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss
Error Detection, Recovery, and Repair in the Translation of Inorganic Nomenclatures, 2. A Proposed Strategy
A Chemical Substructure Search System Based on Chemical Abstracts Index Nomenclature
New Publicly Available Chemical Query Language, CSRML, To Support Chemotype Representations for Application to Data Mining and Modeling
An algorithm for chemical superstructure searching
QSAR Modeling of in Vitro Inhibition of Cytochrome P450 3A4
Application of Graph Theory to Chemical Kinetics, Part 2. Topological Specificity of Single-Route Reaction Mechanisms
Design of Recyclable Plastics with Machine Learning and Genetic Algorithm
The NCI Drug Information System. 2. DIS pre-registry
The Coding of the Three-Dimensional Structure of Molecules by Molecular Transforms and Its Application to Structure-Spectra Correlations and Studies of Biological Activity
OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design
Quantum Mechanics/Molecular Mechanics Modeling of Covalent Addition between EGFR-Cysteine 797 and N -(4-Anilinoquinazolin-6-yl) Acrylamide
Modular Chemical Descriptor Language (MCDL): Composition, Connectivity, and Supplementary Modules
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds