yusuke1997/dblp-id-title huggingface dataset:
Turbocharging Matched Molecular Pair Analysis: Optimizing the Identification and Analysis of Pairs
Improving the Performance of Molecular Dynamics Simulations on Parallel Clusters
Chemical Similarity Searching
Property Prediction for Complex Compounds Using Structure-Free Mendeleev Encoding and Machine Learning
A Computer-Oriented Linear Canonical Notational System for the Representation of Organic Structures with Stereochemistry
Analysis of Commercial and Public Bioactivity Databases
Experimental Program for Online Access to ACS Primary Documents
Estimating Change in Foldability Due to Multipoint Deletions in Protein Structures
Determining the Number of Resonance Structures in Concealed Non-Kekuléan Benzenoid Hydrocarbons
3DFS: A New 3D Flexible Searching System for Use in Drug Design
Phosphorylation Regulation on the Homo-Dimeric Binding of Transactive Response DNA-Binding Protein
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock
Evolutionary Design of Molecules with Desired Properties Using the Genetic Algorithm
Modeling Protein-Glycan Interactions with HADDOCK
Potency Prediction of β-Secretase (BACE-1) Inhibitors Using Density Functional Methods
SeqMG-RPI: A Sequence-Based Framework Integrating Multi-Scale RNA Features and Protein Graphs for RNA-Protein Interaction Prediction
Multi-Knowledge Graph and Multi-View Entity Feature Learning for Predicting Drug-Related Side Effects
Discovery of 2-Acylaminothiophene-3-Carboxamides as Multitarget Inhibitors for BCR-ABL Kinase and Microtubules
Testing Assumptions and Hypotheses for Rescoring Success in Protein-Ligand Docking
Multitask Learning on Graph Convolutional Residual Neural Networks for Screening of Multitarget Anticancer Compounds
AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters
A General Sequence Processing and Analysis Program for Protein Engineering
Toxic Colors: The Use of Deep Learning for Predicting Toxicity of Compounds Merely from Their Graphic Images
Structure-Based Fragment Hopping for Lead Optimization Using Predocked Fragment Database
Bidirectional Molecule Generation with Recurrent Neural Networks
Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning
Intramolecular and Water Mediated Tautomerism of Solvated Glycine
Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation
ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions
SYNGEN program for synthesis design: basic computing techniques
Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network
Numerical Errors and Chaotic Behavior in Docking Simulations
"In Silico" Design of New Uranyl Extractants Based on Phosphoryl-Containing Podands: QSPR Studies, Generation and Screening of Virtual Combinatorial Library, and Experimental Tests
Metabolism Site Prediction Based on Xenobiotic Structural Formulas and PASS Prediction Algorithm
Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries
Electrochemistry Journals
Ordinal Confidence Level Assignments for Regression Model Predictions
Comparative Study of Multitask Toxicity Modeling on a Broad Chemical Space
Thermodynamic Characterization of New Positive Allosteric Modulators Binding to the Glutamate Receptor A2 Ligand-Binding Domain: Combining Experimental and Computational Methods Unravels Differences in Driving Forces
Tuning Neural and Fuzzy-Neural Networks for Toxicity Modeling
Correction of Temperature Variations in Kinetic-Based Determinations by Use of Pruning Computational Neural Networks in Conjunction with Genetic Algorithms
Building a Knowledge-Based Statistical Potential by Capturing High-Order Inter-residue Interactions and its Applications in Protein Secondary Structure Assessment
Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations
Local Electronic Charge Transfer in the Helical Induction of Cis-Transoid Poly(4-carboxyphenyl)acetylene by Chiral Amines
Information Content in Organic Molecules: Brownian Processing at Low Levels
Maximum Spectrum of Continuous Wavelet Transform and Its Application in Resolving an Overlapped Signal
Understanding the Contributions of Microscopic Heat Transfer to Thermal Conductivities of Liquid Aldehydes and Ketones by Molecular Dynamics Simulation
Structural studies of the role of the active site metal in metalloenzymes
Anti-arrhythmic Medication Propafenone a Potential Drug for Alzheimer's Disease Inhibiting Aggregation of Aβ: In Silico and in Vitro Studies
Structure-Based Reaction Descriptors for Predicting Rate Constants by Machine Learning: Application to Hydrogen Abstraction from Alkanes by CH 3 /H/O Radicals
Prediction of p K a Values for Aliphatic Carboxylic Acids and Alcohols with Empirical Atomic Charge Descriptors
Predicting In Vivo Compound Brain Penetration Using Multi-task Graph Neural Networks
Prediction of Aqueous Solubility of Organic Compounds by the General Solubility Equation (GSE)
Computer perception of constitutional (topological) symmetry: TOPSYM, a fast algorithm for partitioning atoms and pairwise relations among atoms into equivalence classes
Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network
Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions
Early Steps in C-Type Inactivation of the hERG Potassium Channel
Integration of microcomputer and mainframe information systems
Integrating Chemo- and Bioinformatics with In Vitro Biological Assays to Discover Potential ACE2 and Mpro Inhibitors against SARS-CoV-2
Symposium on Information Handling and Processing by the Food and Drug Administration Introductory Remarks
Using a Genetic Algorithm To Suggest Combinatorial Libraries
Materials Precursor Score: Modeling Chemists' Intuition for the Synthetic Accessibility of Porous Organic Cage Precursors
Mechanism of Uncoupled Carbocyclization and Epimerization Catalyzed by Two Non-Heme Iron/α-Ketoglutarate Dependent Enzymes
Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis
Revisiting Protein-Protein Docking: A Systematic Evaluation Framework
Proteochemometric Recognition of Stable Kinase Inhibition Complexes Using Topological Autocorrelation and Support Vector Machines
Chemical Topic Modeling: Exploring Molecular Data Sets Using a Common Text-Mining Approach
Use of Topostructural, Topochemical, and Geometric Parameters in the Prediction of Vapor Pressure: A Hierarchical QSAR Approach
External Factor Variable Connectivity Index
Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings
Site of Tagging Influences the Ochratoxin Recognition by Peptide NFO4: A Molecular Dynamics Study
Mechanism-Driven Features Enable Asn Deamidation Reactivity Prediction via Machine Learning Methods
CNSGT: Generative Transformer for De Novo Drug Design Targeting the Central Nervous System
Interpretable Perturbator for Variable Selection in near-Infrared Spectral Analysis
Probe Substrate Dependencies in CYP3A4 Allosteric Inhibition: A Novel Molecular Mechanism Involving F-F′ Loop Perturbations
Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery
Soft Matter under Pressure: Pushing Particle-Field Molecular Dynamics to the Isobaric Ensemble
Dynamic Simulations of Interaction of the PEG-DPPE Micelle-Encapsulated Short-Chain Ceramides with the Raft-Included Membrane
The Discrimination Ability of Some Topological and Information Distance Indices for Graphs of Unbranched Hexagonal Systems
Using Information from Historical High-Throughput Screens to Predict Active Compounds
From Proteins to Ligands: Decoding Deep Learning Methods for Binding Affinity Prediction
Chapman and Hall Dictionary of Organic Compounds on CD-ROM
Calculating the cell polynomial of catacondensed polycyclic hydrocarbons. [Erratum to document cited in CA120: 190658]
Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations
Anisotropic Solvent Model of the Lipid Bilayer. 1. Parameterization of Long-Range Electrostatics and First Solvation Shell Effects
How Do Food Compounds Interact with Their Protein Targets? Alternative Modes for Protein Binding
PySSA for Windows: End-User Protein Structure Prediction and Visual Analysis with ColabFold and PyMOL
Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds
Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis
Enumeration of Virtual Libraries of Combinatorial Modular Macrocyclic (Bracelet, Necklace) Architectures and Their Linear Counterparts
Introduction to Programming with Fortran: With Coverage of Fortran 90, 95, 2003 and 77. By Ian Chivers and Jane Sleightholme. Springer: London, U.K., 2005. XX+592 pp and CD-ROM. ISBN 1-84628-053-5. Softcover. U.S. $69.95, Euro 53.45
Application of genetic algorithms in the field of constitutional similarity
Computational Estimation of Lanthanoid-Water Bond Lengths by Semiempirical Methods
Random Forest: A Classification and Regression Tool for Compound Classification and QSAR Modeling
GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules
Similarity and the Beilstein Information System: Searching for concepts with current facts
Structure-Activity Correlation of Flavone Derivatives for Inhibition of cAMP Phosphodiesterase
HNet-DNN: Inferring New Drug-Disease Associations with Deep Neural Network Based on Heterogeneous Network Features
Correction to Computational Comparison of Imidazoline Association with the I2 Binding Site in Human Monoamine Oxidases
ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches
Special Features of NBS's Omnidata System Applicable to the Retrieval, Analysis, and Dissemination of Chemical Data
Mining the Characteristic Interaction Patterns on Protein-Protein Binding Interfaces
Separation Selectivity of CH4/CO2 Gas Mixtures in the ZIF-8 Membrane Explored by Dynamic Monte Carlo Simulations
Comparison of three different approaches to the property prediction problem
AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening
Computer-Based Structure Determination: Then and Now
Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis
Assessment of the Fragment Docking Program SEED
Structure Generation from a Gross Formula. 7. Graph Isomorphism: A Consequence of the Vertex Equivalence
QSAR Modeling Using Automatically Updating Correction Libraries: Application to a Human Plasma Protein Binding Model
EndNote Plus 2.1 for Windows 3.1
Extensions of the Wiener Number
Walk Numbers eWM: Wiener-Type Numbers of Higher Rank
Computational Chemistry in Asia
Performance of the LRESC Model on top of DFT Functionals for Relativistic NMR Shielding Calculations
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs
Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2
FESTA: A Polygon-Based Approach for Extracting Relevant Structures from Free Energy Surfaces Obtained in Molecular Simulations
A Grid Map Based Approach to Identify Nonobvious Ligand Design Opportunities in 3D Protein Structure Ensembles
PEARLS: Program for Energetic Analysis of Receptor-Ligand System
Prediction of Substrates for Glutathione Transferases by Covalent Docking
Subgraph Topology and Dynamic Graph Topology Enhanced Graph Learning and Pairwise Feature Context Relationship Integration for Predicting Disease-Related miRNAs
Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors
Quality Threshold Clustering of Molecular Dynamics: A Word of Caution
Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields
Modeling the Hydrolysis of Iron-Sulfur Clusters
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities
REINVENT 2.0: An AI Tool for De Novo Drug Design
Algebraic Kekulé Formulas for Benzenoid Hydrocarbons
Exploring Peptide's Antifreeze Activity Using a Semi-Automated Molecular Dynamics-Enabled Screening Framework
Interaction Entropy for Computational Alanine Scanning
A Comparison of Partial Order Technique with Three Methods of Multi-Criteria Analysis for Ranking of Chemical Substances
FragExplorer: GRID-Based Fragment Growing and Replacement
Feature Engineering for Materials Chemistry - Does Size Matter?
Computer translation of IUPAC systematic organic chemical nomenclature. 3. Syntax analysis and semantic processing
An expert-database system for sample preparation by microwave dissolution. 2. Electronic transfer and implementation of standard methods
Identification and Experimental Validation of NETosis-Mediated Abdominal Aortic Aneurysm Gene Signature Using Multi-omics, Machine Learning, and Mendelian Randomization
Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration
FraHMT: A Fragment-Oriented Heterogeneous Graph Molecular Generation Model for Target Proteins
Identification of Potential TMPRSS2 Inhibitors for COVID-19 Treatment in Chinese Medicine by Computational Approaches and Surface Plasmon Resonance Technology
Predicting Caco-2 Cell Permeation Coefficients of Organic Molecules Using Membrane-Interaction QSAR Analysis
FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening
A Proposed Common Spatial Pharmacophore and the Corresponding Active Conformations of Some TxA2 Receptor Antagonists
Ligand-Steered Modeling and Docking: A Benchmarking Study in Class A G-Protein-Coupled Receptors
An Anchor-Dependent Molecular Docking Process for Docking Small Flexible Molecules into Rigid Protein Receptors
On Hall and Kier's Topological State and Total Topological Index
Adapting the Gmelin Handbook to Modern Information Requirements
Modeling and Benchmark Data Set for the Inhibition of c-Jun N-terminal Kinase-3
General Purpose 2D and 3D Similarity Approach to Identify hERG Blockers
Chemical Reactions Information Retrieval from Chemical Abstracts Service Publications and Services
Correction to "De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder"
E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning
Microscopic Understanding of the Conformational Stability of the Aggregated Nonamyloid β Components of α-Synuclein
Automatic Strategy in Computer Design of Synthesis: An Example of Organophosphorus Chemistry
Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach
A microcomputer-based system for chemical information and molecular structure search
Three Simple Properties Explain Protein Stability Change upon Mutation
AIDDISON: Empowering Drug Discovery with AI/ML and CADD Tools in a Secure, Web-Based SaaS Platform
Bioassay-Guided Isolation and in Silico Study of Antibacterial Compounds From Petroleum Ether Extract of Peperomia blanda (Jacq.) Kunth
Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning
Structure-Activity Relationships in Non-Ligand Binding Pocket (Non-LBP) Diarylhydrazide Antiandrogens
Nonbonded Force Field Parameters from Minimal Basis Iterative Stockholder Partitioning of the Molecular Electron Density Improve CB7 Host-Guest Affinity Predictions
Modeling Kinase Inhibition Using Highly Confident Data Sets
Structure-Based Pharmacophore Design and Virtual Screening for Novel Angiotensin Converting Enzyme 2 Inhibitors
Determination of Urinary Calcium-Oxalate Formation Risk with BONN-Risk-Index and EQUIL Applied to a Family
Discovery of Potent Selective HDAC6 Inhibitors with 5-Phenyl-1 H -indole Fragment: Virtual Screening, Rational Design, and Biological Evaluation
Corel WordPerfect X5
Integrating Data Mining and Natural Language Processing to Construct a Melting Point Database for Organometallic Compounds
Selecting Collective Variables and Free-Energy Methods for Peptide Translocation across Membranes
Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design
De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping
A Toxicity Evaluation and Predictive System Based on Neural Networks and Wavelets
Conformation and Permeability: Cyclic Hexapeptide Diastereomers
Multi-Assay-Based Compound Prioritization via Assistance Utilization: A Machine Learning Framework
ColBioS-FlavRC: A Collection of Bioselective Flavonoids and Related Compounds Filtered from High-Throughput Screening Outcomes
Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides
Exploring Alternative Strategies for the Identification of Potent Compounds Using Support Vector Machine and Regression Modeling
New Born Radii Deriving Method for Generalized Born Model
Predicting Binding Poses and Affinities in the CSAR 2013-2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential
Application of the PharmPrint Methodology to Two Protein Kinases
Fentanyl and the Fluorinated Fentanyl Derivative NFEPP Elicit Distinct Hydrogen-Bond Dynamics of the Opioid Receptor
Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery
A Procedure for Characterization of the Rings of a Molecule
Deciphering the Mechanism of Binding Selectivity of Chlorofluoroacetamide-Based Covalent Inhibitors toward L858R/T790M Resistance Mutation
Gas-Phase and Solution Conformations of Selected Dimeric Structural Units of Heparin
DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space
Cell-Integral-Diversity Criterion: A Proposal for Minimizing Cluster Artifact in Cell-Based Selections
Tautomer Standardization in Chemical Databases: Deriving Business Rules from Quantum Chemistry
Automated Docking with Protein Flexibility in the Design of Femtomolar "Click Chemistry" Inhibitors of Acetylcholinesterase
Scaffold-Focused Virtual Screening: Prospective Application to the Discovery of TTK Inhibitors
DeepNCI: DFT Noncovalent Interaction Correction with Transferable Multimodal Three-Dimensional Convolutional Neural Networks
Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening
Applying Molecular Dynamics Simulations to Unveil the Anisotropic Growth Mechanism of Gold Nanorods: Advances and Perspectives
Review of ring perception algorithms for chemical graphs
Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications
Accurate and Fast Prediction of Intrinsically Disordered Protein by Multiple Protein Language Models and Ensemble Learning
Investigation of Structural Mechanisms Underlying p53 Dysfunction Caused by 148 Missense Mutations Using AlphaFold3 and Molecular Dynamics Simulations
Molecular Field Extrema as Descriptors of Biological Activity: Definition and Validation
Developing Hybrid Machine Learning Frameworks for Polymer Property Prediction Based on Composition and Sequence Features
The PESTICIDES Disk
Predicting Regioselectivity of Cytosolic Sulfotransferase Metabolism for Drugs
Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems
Meta-Code for Systematic Analysis of Chemical Addition (SACHA): Application to Fluorination of C 70 and Carbon Nanostructure Growth
Toward Accurate PAH IR Spectra Prediction: Handling Charge Effects with Classical and Deep Learning Models
Characterization of Isospectral Graphs Using Graph Invariants and Derived Orthogonal Parameters
How Far Are Molecular Connectivity Descriptors from IS Molecular Pseudoconnectivity Descriptors?
Molecular Shape Profiles
DIA-DB: A Database and Web Server for the Prediction of Diabetes Drugs
MCSS: a new algorithm for perception of maximal common substructures and its application to NMR spectral studies. 1. The algorithm
New Insights on the Reaction Pathway Leading to Lactyl-ThDP: A Theoretical Approach
Perturbation-Response Scanning Reveals Key Residues for Allosteric Control in Hsp70
A Rapid Generalized Minicomputer Text Search System Incorporating Algebraic Entry of Boolean Strategies
inSARa: Intuitive and Interactive SAR Interpretation by Reduced Graphs and Hierarchical MCS-Based Network Navigation
SynRoute: A Retrosynthetic Planning Software
An Integrated Virtual Screening Approach for VEGFR-2 Inhibitors
What Are the Odds of Finding a COVID-19 Drug from a Lab Repurposing Screen?
Ramachandran-like Conformational Space for DNA
Universal Activation Index for Class A GPCRs
Combining Data-Driven and Structure-Based Approaches in Designing Dual PARP1-BRD4 Inhibitors for Breast Cancer Treatment
Dissecting the RAD51-BRC4 Interaction Landscape through Integrative Molecular Simulations and Experimental Biophysics
Generalized Topological Indices. Modeling Gas-Phase Rate Coefficients of Atmospheric Relevance
NovoFLAP: A Ligand-Based De Novo Design Approach for the Generation of Medicinally Relevant Ideas
Perturbation of Fluid Dynamics Properties of Water Molecules during G Protein-Coupled Receptor-Ligand Recognition: The Human A 2A Adenosine Receptor as a Key Study
SARVision Plus by ChemApps
New Strategy for Receptor-Based Pharmacophore Query Construction: A Case Study for 5-HT 7 Receptor Ligands
Essential Oils as Antimicrobials against Acinetobacter baumannii : Experimental and Literature Data to Definite Predictive Quantitative Composition-Activity Relationship Models Using Machine Learning Algorithms
Two-Dimensional Arrays in the Analysis of Trends in Series of Molecules: Strongly Subspectral Molecular Graphs, Formula Periodic Tables, and Number of Resonance Structures
GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking
Structure-Based Drug Design of Diphenyl α-Aminoalkylphosphonates as Prostate-Specific Antigen Antagonists
Development of New Inhibitors of HDAC1-3 Enzymes Aided by In Silico Design Strategies
Machine Learning-Guided High-Throughput Screening of Metal-Organic Frameworks for Atmospheric Ozone Capture: A Computational Materials Informatics Approach
Fast Local Alignment of Protein Pockets (FLAPP): A System-Compiled Program for Large-Scale Binding Site Alignment
Maximum Common Substructures of Organic Compounds Exhibiting Similar Infrared Spectra
MMSG-DTA: A Multimodal, Multiscale Model Based on Sequence and Graph Modalities for Drug-Target Affinity Prediction
Correction to Modules Identification in Protein Structures: The Topological and Geometrical Solutions
Distance Dependent Scoring Function for Describing Protein-Ligand Intermolecular Interactions
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR
Aliphatic Polyester Recognition and Reactivity at the Active Cleft of a Fungal Cutinase
Computer assisted analysis of reactions involving organic free radicals and diradicals
The Identification of Ligand Features Essential for PXR Activation by Pharmacophore Modeling
Computational Predictions of Nonclinical Pharmacokinetics at the Drug Design Stage
Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models
Theorems on Molecular Shape-Similarity Descriptors: External T-Plasters and Interior T-Aggregates
F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization
Elucidation of Characteristic Structural Features of Ligand Binding Sites of Protein Kinases: A Neural Network Approach