yusuke1997/dblp-id-title huggingface dataset:
Combining Ligand- and Structure-Based Approaches for the Discovery of New Inhibitors of the EPHA2-ephrin-A1 Interaction
Activity-Aware Clustering of High Throughput Screening Data and Elucidation of Orthogonal Structure-Activity Relationships
Analysis of the Fragmentation Pathways for the Collision-Induced Dissociation of Protonated Cyclophosphamide: A Mass Spectrometry and Quantum Mechanical Study
Open Computing Grid for Molecular Science and Engineering
Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ 42 Peptide Monomer Conformations
Integrating Mechanistic and Toxicokinetic Information in Predictive Models of Cholestasis
Combined Computational-Biochemical Approach Offers an Accelerated Path to Membrane Protein Solubilization
Multivariate Regression Outperforms Several Robust Architectures of Neural Networks in QSAR Modeling
A Comparative Study on the Application of Hierarchical-Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs
Growth in Catacondensed Benzenoid Graphs
Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR-Ligand Recognition Pathway in a Nanosecond Time Scale
Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring
Protease Inhibitors in View of Peptide Substrate Databases
Congruence Relations for the Wiener Index of Hexagonal Chains
Manual Construction and Mathematics- and Computer-Aided Counting of Stereoisomers. The Example of Oligoinositols
iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides
Copper(II) Ion Binding to Cellular Prion Protein
Microbial Pathway Prediction: A Functional Group Approach
Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization
Impact of Protein Preparation on Resulting Accuracy of FEP Calculations
Virtual Compound Libraries: A New Approach to Decision Making in Molecular Discovery Research
Planning the Proposed National Resource for Computation in Chemistry
Analysis of the Flow Patterns of Liquid Organic Compounds between Blade Electrodes by Classification Models
Houben-Weyl and Science of Synthesis , Web Versions
Evaluation of Virtual Screening as a Tool for Chemical Genetic Applications
Search for Predictive Generic Model of Aqueous Solubility Using Bayesian Neural Nets
Bayesian Similarity Searching in High-Dimensional Descriptor Spaces Combined with Kullback-Leibler Descriptor Divergence Analysis
A Formal Comparison between Molecular Quantum Similarity Measures and Indices
Computer Generation of Nuclear Equivalence Classes Based on the Three-Dimensional Molecular Structure
Efficient Exploration of High-Dimensional Configuration Spaces for the Generation of Chemical Datasets
New method for the calculation of bond native polarity using molecular electronic energy
Probing the Bioactivity-Relevant Chemical Space of Robust Reactions and Common Molecular Building Blocks
How to Compute Atomistic Insight in DFT Clusters: The REG-IQA Approach
The Overall Wiener Index-A New Tool for Characterization of Molecular Topology
Statistical Analysis and Prediction of Covalent Ligand Targeted Cysteine Residues
Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
Heats of Formation of Polyhex Polycyclic Aromatic Hydrocarbons from Their Adjacency Matrixes
Looking Back to the Future: Predicting in Vivo Efficacy of Small Molecules versus Mycobacterium tuberculosis
Incorporating Multisource Knowledge To Predict Drug Synergy Based on Graph Co-regularization
Automatic Prediction of Peak Optical Absorption Wavelengths in Molecules Using Convolutional Neural Networks
A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations
Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase
De Novo Drug Design Using Multiobjective Evolutionary Graphs
A Different Method for Steric Field Evaluation in CoMFA Improves Model Robustness
De Novo Generation of Molecular Structures Using Optimization To Select Graphs on a Given Lattice
Mining for Bioactive Scaffolds with Scaffold Networks: Improved Compound Set Enrichment from Primary Screening Data
MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search
Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks
A Comparative Study on Feature Selection Methods for Drug Discovery
Rational Design of New Class of BH3-Mimetics As Inhibitors of the Bcl-x L Protein
Graph Curvature Flow-Based Masked Attention
Identification of Enolase 1 as a Potential Target for Magnaporthe oryzae : Integrated Proteomic and Molecular Dynamics Simulation
Improving the Predicting Power of Partial Order Based QSARs through Linear Extensions
Quantifying Inter-Residue Contacts through Interaction Energies
UniBioPAN: A Novel Universal Classification Architecture for Bioactive Peptides Inspired by Video Action Recognition
Prediction of Supercritical Carbon Dioxide Solubility of Organic Compounds from Molecular Structure
Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets
HIV OctaScanner: A Machine Learning Approach to Unveil Proteolytic Cleavage Dynamics in HIV-1 Protease Substrates
The Application of Neural Networks in Conformational Analysis, 1. Prediction of Minimum and Maximum Interatomic Distances
Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design
Prediction of Loops in G Protein-Coupled Receptor Homology Models: Effect of Imprecise Surroundings and Constraints
Correction to "Exploration of SARS-CoV-2 3CL pro Inhibitors by Virtual Screening Methods, FRET Detection, and CPE Assay"
Toward Assay-Aware Bioactivity Model(er)s: Getting a Grip on Biological Context
ProcessOptimizer, an Open-Source Python Package for Easy Optimization of Real-World Processes Using Bayesian Optimization: Showcase of Features and Example of Use
HessFit: A Toolkit to Derive Automated Force Fields from Quantum Mechanical Information
Ensemble Feature Selection: Consistent Descriptor Subsets for Multiple QSAR Models
Analysis of Similarity/Dissimilarity of DNA Sequences Based on Nonoverlapping Triplets of Nucleotide Bases
A Computational Study of the Effectiveness of the Frontier Molecular Orbital Formalism in Predicting Conformational Isomerism in (p-RC6H4NC)2W(dppe)2
TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics
MolAgent: Biomolecular Property Estimation in the Agentic Era
Catching Functional Modes and Structural Communication in Dbl Family Rho Guanine Nucleotide Exchange Factors
Evaluation of Open-Source Large Language Models for Metal-Organic Frameworks Research
ACS Committee on Nomenclature Annual Report for 1977
Calculating Single-Channel Permeability and Conductance from Transition Paths
Novel Approach to Structure-Based Pharmacophore Search Using Computational Geometry and Shape Matching Techniques
Description of organic reactions based on imaginary transition structures. 1. Introduction of new concepts
Computational Prediction and Biochemical Analyses of New Inverse Agonists for the CB1 Receptor
Fuzzy Matched Pairs: A Means To Determine the Pharmacophore Impact on Molecular Interaction
The Often-Overlooked Power of Summary Statistics in Exploratory Data Analysis: Comparison of Pattern Recognition Entropy (PRE) to Other Summary Statistics and Introduction of Divided Spectrum-PRE (DS-PRE)
Chemical Potential Differences in the Macroscopic Limit from Fluctuations in Small Systems
Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes
Bidirectional Long Short-Term Memory (BiLSTM) Neural Networks with Conjoint Fingerprints: Application in Predicting Skin-Sensitizing Agents in Natural Compounds
Education Program for Macromolecules Structure Examination
A High-Resolution Shape-Fragment MEDLA Database for Toxicological Shape Analysis of PAHs
Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases
Autogenerating a Domain-Specific Question-Answering Data Set from a Thermoelectric Materials Database to Enable High-Performing BERT Models
OpenMMDL - Simplifying the Complex: Building, Simulating, and Analyzing Protein-Ligand Systems in OpenMM
RhoMax: Computational Prediction of Rhodopsin Absorption Maxima Using Geometric Deep Learning
PRA-MutPred: Predicting the Effect of Point Mutations in Protein-RNA Complexes Using Structural Features
Clustering and Rule-Based Classifications of Chemical Structures Evaluated in the Biological Activity Space
Effect of Size and Shape of Nitrogen-Containing Aromatics on Conformational Preferences of DNA Containing Damaged Guanine
Local and Global Motions Underlying Antibiotic Binding in Bacterial Ribosome
The Eighteenth International Course & Conference on the Interfaces among Mathematics, Chemistry & Computer Sciences June 23-28, 2003 Dubrovnik, Croatia
Discovery of Potent Covalent CRM1 Inhibitors Via a Customized Structure-Based Virtual Screening Pipeline and Bioassays
Application of Chemical Graph Theory for Automated Mechanism Generation
Computerized Molecular Modeling as a Tool To Improve Chemistry Teaching
Dimerization of α-Synuclein Fragments Studied by Isothermal-Isobaric Replica-Permutation Molecular Dynamics Simulation
Rapid Exploration of the Assembly Chemical Space of Molecular Graphs
Evaluation of Quantitative Structure-Activity Relationship Modeling Strategies: Local and Global Models
On The Radical Scavenging and DNA Repairing Activities by Natural Oxygenated Diterpenoids: Theoretical Insights
Breaking Down the Bottlebrush: Atomically Detailed Structural Dynamics of Mucins
AMPGP: Discovering Highly Effective Antimicrobial Peptides via Deep Learning
Molecular Binding Sites Are Located Near the Interface of Intrinsic Dynamics Domains (IDDs)
Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site
On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate
When the Position of Pendant Groups Makes the Difference in G-Quadruplex Behavior: The Case of Bis-Conjugated Thrombin-Binding Aptamers
Site-of-Metabolism Prediction with Aleatoric and Epistemic Uncertainty Quantification
Information and Organic Molecules: Structure Considerations via Integer Statistics
Molecular substructure searching: minicomputer-based query execution
Conformation Control of Abiotic α-Helical Foldamers
Proteomic Learning of Gamma-Aminobutyric Acid (GABA) Receptor-Mediated Anesthesia
Benchmarking AlphaFold-Generated Structures of Chemokine-Chemokine Receptor Complexes
ZINC Express: A Virtual Assistant for Purchasing Compounds Annotated in the ZINC Database
Single-Image Super-Resolution Improvement of X-ray Single-Particle Diffraction Images Using a Convolutional Neural Network
Prediction of Activity Cliffs Using Condensed Graphs of Reaction Representations, Descriptor Recombination, Support Vector Machine Classification, and Support Vector Regression
MFGNN-DSA: A Model for Predicting Drug-Side Effect Associations via Multifeature Fusion and Graph Neural Networks
Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein-Ligand Binding and Competitive Binding
Global Optimization of Lennard-Jones Clusters by a Parallel Fast Annealing Evolutionary Algorithm
High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
An algorithm for the multiple common subgraph problem
Multimerizations, Aggregation, and Transfer Reactions of Small Numbers of Molecules
Computer representation of generic chemical structures by an extended block-cutpoint tree
Size-Dependent Conformational Features of Aβ 17-42 Protofilaments from Molecular Simulation Studies
DRPMKB1.0: A Comprehensive Knowledge Base for an AI-Oriented Drug Repositioning Prediction Model
ALCHEMY
Determining the Degree of Randomness of Descriptors in Linear Regression Equations with Respect to the Data Size
The Derivation of a Matched Molecular Pairs Based ADME/Tox Knowledge Base for Compound Optimization
Unsupervised Machine Learning-Based Image Recognition of Raw Infrared Spectra: Toward Chemist-like Chemical Structural Classification and Beyond Numerical Data
Computer translation of inorganic chemical nomenclature to a dynamic abstract data structure
Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS
Modification of Wiener Index and Its Application
Integration of an Inhibitor-like Rule and Structure-based Virtual Screening for the Discovery of Novel Myeloperoxidase Inhibitors
Electron-Passing Neural Networks for Atomic Charge Prediction in Systems with Arbitrary Molecular Charge
G2GT: Retrosynthesis Prediction with Graph-to-Graph Attention Neural Network and Self-Training
What's What: The (Nearly) Definitive Guide to Reaction Role Assignment
A Protein Folding Degree Measure and Its Dependence on Crystal Packing, Protein Size, Secondary Structure, and Domain Structural Class [ J. Chem. Inf. Comput. Sci, 44, 1238-1250 (2004)]
A 3D QSAR Study on a Set of Dopamine D 4 Receptor Antagonists
Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents
APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories
Prediction of Henry's Law Constants by a Quantitative Structure Property Relationship and Neural Networks
Deep-Learning Potential Molecular Dynamics Study on Nanopolycrystalline Al-Er Alloys: Effects of Er Concentration, Grain Boundary Segregation, and Grain Size on Plastic Deformation
Why Does the E1219V Mutation Expand T-Rich PAM Recognition in Cas9 from Streptococcus pyogenes ?
In Silico Identification of a Key Residue for Substrate Recognition of the Riboflavin Membrane Transporter RFVT3
Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides
Binding Selectivity Studies of Phosphoinositide 3-Kinases Using Free Energy Calculations
Different Discrete Wavelet Transforms Applied to Denoising Analytical Data
A Simplified Algorithm Using Base 5 Numbers To Assign Canonical Names to Cata-Condensed Polybenzenes
Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation
Real number vertex invariants: Regressive distance sums and related topological indexes
Reaction Site Mapping of Xenobiotic Biotransformations
PPDock: Pocket Prediction-Based Protein-Ligand Blind Docking
Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches
Deconstructing 1 H NMR Chemical Shifts in Strong Hydrogen Bonds: A Computational Investigation of Solvation, Dynamics, and Nuclear Delocalization Effects
Chemical Fragment Generation and Clustering Software
E-State Modeling of Dopamine Transporter Binding. Validation of the Model for a Small Data Set
VenomPred 2.0: A Novel In Silico Platform for an Extended and Human Interpretable Toxicological Profiling of Small Molecules
A user's view of chemical reaction information sources
Creating Artificial Binding Pocket Boundaries To Improve the Efficiency of Flexible Ligand Docking
Identification of Novel Malarial Cysteine Protease Inhibitors Using Structure-Based Virtual Screening of a Focused Cysteine Protease Inhibitor Library
Toward Predicting Intermetallics Surface Properties with High-Throughput DFT and Convolutional Neural Networks
OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data
HydroLayer Calculator: A Pseudo-Parallel Tool for Rapid Hydration Layer Structure Calculation in MD Simulations via VMD
GARLig: A Fully Automated Tool for Subset Selection of Large Fragment Spaces via a Self-Adaptive Genetic Algorithm
Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors
Chemical Graphs: Looking Back and Glimpsing Ahead
An Efficient Design for Chemical Structure Searching. I. The Screens
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA-Protein Interaction Prediction
Similarity searching on CAS Registry substances. 1. Global molecular property and generic atom triangle geometric searching
A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations
PLANET: A Multi-objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction
Building and structuring a large knowledge base for computer-assisted synthesis planning
Multi-Peptide: Multimodality Leveraged Language-Graph Learning of Peptide Properties
Recent ASTM standardization developments for chemical information
Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air
Spectrum Digitizing and Conditioning for the Infrared Library of Amorphous Silicon Alloys
Simple Structure-Based Approach for Predicting the Activity of Inhibitors of Beta-Secretase (BACE1) Associated with Alzheimer's Disease
On-Line Indexing Experiment at Chemical Abstracts Service: Algorithmic Generations of Articulated Index Entries from Natural Language Phrases
Ligand- and Structure-Based Virtual Screening for Clathrodin-Derived Human Voltage-Gated Sodium Channel Modulators
Characterization of DNA Primary Sequences by a New Similarity/Diversity Measure Based on the Partial Ordering
TCN-RDP: Predicting Drug-Induced Liver Injury from Time-Series Toxicogenomic Data
RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry
Solution-Binding and Molecular Docking Approaches Combine to Provide an Expanded View of Multidrug Recognition in the MDR Gene Regulator BmrR
Identification of Robust Antibiotic Subgroups by Integrating Multi-Species Drug-Drug Interactions
Algorithm for Reaction Classification
Separation of the Energetic and Geometric Contributions to Aromaticity, 2. Analysis of the Aromatic Character of Benzene Rings in Their Various Topological Environments in the Benzenoid Hydrocarbons. Crystal and Molecular Structure of Coronene
In Silico Prediction of Buffer Solubility Based on Quantum-Mechanical and HQSAR- and Topology-Based Descriptors
EnzyACT: A Novel Deep Learning Method to Predict the Impacts of Single and Multiple Mutations on Enzyme Activity
Resolving multiple overlapping calorimetric transitions by use of a microcomputer: studies on erythrocyte membranes
Problems in the computerization of chemical information: capture of tabular and graphical data
Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes
Incorporating Anionic Ligands in Chemical Space Exploration with New Ligand Additivity Relationships
RAG_MCNNIL6: A Retrieval-Augmented Multi-Window Convolutional Network for Accurate Prediction of IL-6 Inducing Epitopes
Anisotropic Network Analysis of Open/Closed HCN4 Channel Advocates Asymmetric Subunit Cooperativity in cAMP Modulation of Gating
Estimation of Hematocrit Volume Using Blood Glucose Concentration through Extreme Gradient Boosting Regressor Machine Learning Model
BioAlmanac [CD-ROM]
Computational Insight into Small Molecule Inhibition of Cyclophilins
Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations
MCMFPP: A Multifunctional Peptides Prediction Method Based on Class Feature Enhancement and Classifier Fusion
Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models
Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent
Web Service Infrastructure for Chemoinformatics
Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa: d-Lac Ligase VanA
Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures
Machine Learning-Based Drug Repositioning of Novel Janus Kinase 2 Inhibitors Utilizing Molecular Docking and Molecular Dynamic Simulation
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1
Auxiliary Discrminator Sequence Generative Adversarial Networks for Few Sample Molecule Generation
Computer Modelling in Inorganic Crystallography. Edited by C. R. A. Catlow. Academic Press: San Diego, 1997, 340 pp. ISBN 0-12-164135-X
Representation of Chemical Structures in Knowledge-Based Systems: The StAR System
Hither-CMI: Prediction of circRNA-miRNA Interactions Based on a Hybrid Multimodal Network and Higher-Order Neighborhood Information via a Graph Convolutional Network
QSAR Models for P-Glycoprotein Transport Based on a Highly Consistent Data Set
A New Class of Superhalogen Based Anion Receptor in Li-Ion Battery Electrolytes
Homology Modeling and Docking Analysis of the Interaction between Polyphenols and Mammalian 20S Proteasomes
Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations
Determination of structural similarity by quantitative comparisons of Wiswesser Line Notation entries
A Computational Approach to the Study of the Binding Mode of S1P1R Agonists Based on the Active-Like Receptor Model
Concerted Interactions between Multiple gp41 Trimers and the Target Cell Lipidome May Be Required for HIV-1 Entry
Importance of Receptor Flexibility in Binding of Cyclam Compounds to the Chemokine Receptor CXCR4
Exploration of Chemical Space Guided by PixelCNN for Fragment-Based De Novo Drug Discovery
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace
Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility
How To Enumerate the Connectional Isomers of a Toroidal Polyhex Fullerene
Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms
CHEMTEXT
COSMO s im : Bioisosteric Similarity Based on COSMO-RS sigma Profiles
Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource
PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks
A Virtual Screening Approach for Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents Based on Docking and Pharmacophore Models
A Multivariate Chemical Similarity Approach to Search for Drugs of Potential Environmental Concern
MolSnapper: Conditioning Diffusion for Structure-Based Drug Design
Yet another linear notation scheme for organic compounds. 1
Virtual Libraries of Tetrapyrrole Macrocycles. Combinatorics, Isomers, Product Distributions, and Data Mining
A Novel Approach to Retrosynthetic Analysis Using Knowledge Bases Derived from Reaction Databases
New Variable Selection Method Using Interval Segmentation Purity with Application to Blockwise Kernel Transform Support Vector Machine Classification of High-Dimensional Microarray Data
Automatic processing of graphics for image databases in science
Density Functional Study of Methane Activation by Frustrated Lewis Pairs with Group 13 Trihalides and Group 15 Pentahalides and a Machine Learning Analysis of Their Barrier Heights
Noncovalent Cross-links in Context with Other Structural and Functional Elements of Proteins
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real