yusuke1997/dblp-id-title huggingface dataset:
Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant
Comment on "The Extent of the Relationship between the Graph-Theoretical and the Geometric Shape Coefficients of Chemical Compounds"
13C NMR Chemical Shift Calculations for Some Substituted Pyridines: A Comparative Consideration
Process-Driven Information Management System at a Biotech Company: Concept and Implementation
ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources
Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4, 5)P 2 Lipids
Applications of Free-Energy Calculations to Biomolecular Processes. A Collection
Highly Predictive CoMFA and CoMSIA Models for Two Series of Stromelysin-1 (MMP-3) Inhibitors Elucidate S1' and S1-S2' Binding Modes
Binding Space Concept: A New Approach To Enhance the Reliability of Docking Scores and Its Application to Predicting Butyrylcholinesterase Hydrolytic Activity
Molecular Dynamics Simulations of the Adenosine A2a Receptor: Structural Stability, Sampling, and Convergence
Extended Ensemble Molecular Dynamics Study of Ammonia-Cellulose I Complex Crystal Models: Free-Energy Landscape and Atomistic Pictures of Ammonia Diffusion in the Crystalline Phase
Database searching on the basis of three-dimensional molecular similarity using the SPERM program
Permutation Invariant Graph-to-Sequence Model for Template-Free Retrosynthesis and Reaction Prediction
Effects of All-Atom and Coarse-Grained Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of a Tau K18 Monomer
Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods
Enumeration of isomers of polyethers
Enhanced SAR Maps: Expanding the Data Rendering Capabilities of a Popular Medicinal Chemistry Tool
A 3D-QSAR Study of Anticoccidial Triazines Using Molecular Shape Analysis
tmQM Dataset - Quantum Geometries and Properties of 86k Transition Metal Complexes
Dielectric Ceramics Database Automatically Constructed by Data Mining in the Literature
Generative AI for the Design of Molecules: Advances and Challenges
Hydration of Aromatic Heterocycles as an Adversary of π-Stacking
Discovery of Covalent Ligands via Noncovalent Docking by Dissecting Covalent Docking Based on a "Steric-Clashes Alleviating Receptor (SCAR)" Strategy
Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3
Chemical substructure searching
Optimizing the Performance of In Silico ADMET General Models According to Local Requirements: MARS Approach. Solubility Estimations As Case Study
G Protein- and Agonist-Bound Serotonin 5-HT 2A Receptor Model Activated by Steered Molecular Dynamics Simulations
How Do Small Molecule Aggregates Inhibit Enzyme Activity? A Molecular Dynamics Study
Building Highly Reliable Quantitative Structure-Activity Relationship Classification Models Using the Rivality Index Neighborhood Algorithm with Feature Selection
ACS Committee on Nomenclature, Annual Report, 1979
Look What You Made Me Do: Discerning Feature for Classification of Endocrine-Disrupting Chemical Binding to Steroid Hormone Receptors
MT-EpiPred: Multitask Learning for Prediction of Small-Molecule Epigenetic Modulators
ComNet: A Multiview Deep Learning Model for Predicting Drug Combination Side Effects
Propagation of Holes and Electrons in Metal-Organic Frameworks
Turning a Mesophilic Protein into a Thermophilic One: A Computational Approach Based on 3D Structural Features
TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features
MORPH: A New Tool for Ligand Design
Molecular Dynamics Simulations of the HIV-1 Integrase Dimerization Interface: Guidelines for the Design of a Novel Class of Integrase Inhibitors
Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases
Rational Design and In Vitro Evaluation of Novel Peptides Binding to Neuroligin-1 for Synaptic Targeting
Models of Steroid Binding Based on the Minimum Deviation of Structurally Assigned 13 C NMR Spectra Analysis (MiDSASA)
Automatically Predicting Material Properties with Microscopic Images: Polymer Miscibility as an Example
ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites
Numerical Determination of the Kekulé Structure Count of Some Symmetrical Polycyclic Aromatic Hydrocarbons and Their Relationship with -Electronic Energy (A Computational Approach)
Bond Contributions to the Wiener Index
Physics-Informed Multifidelity Gaussian Process: Modeling the Effect of Water and Temperature on the Viscosity of a Deep Eutectic Solvent
New Features of the Open Source Monte Carlo Software Brick-CFCMC: Thermodynamic Integration and Hybrid Trial Moves
Decision Forest: Combining the Predictions of Multiple Independent Decision Tree Models
Treating Chemical Diversity in QSAR Analysis: Modeling Diverse HIV-1 Integrase Inhibitors Using 4D Fingerprints
Bidirectional Graphormer for Reactivity Understanding: Neural Network Trained to Reaction Atom-to-Atom Mapping Task
Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation
Medicinal Chemists versus Machines Challenge: What Will It Take to Adopt and Advance Artificial Intelligence for Drug Discovery?
A Representation of p Systems for Efficient Computer Manipulation
Diff-SE: A Diffusion-Augmented Contrastive Learning Framework for Super-Enhancer Prediction
MELD in Action: Harnessing Data to Accelerate Molecular Dynamics
In Silico Drug Screening Approach for the Design of Magic Bullets: A Successful Example with Anti-HIV Fullerene Derivatized Amino Acids
Streamlining Large Chemical Library Docking with Artificial Intelligence: the PyRMD2Dock Approach
Conformational Determinants of the Activity of Antiproliferative Factor Glycopeptide
Simulation of the Adsorption and Release of Large Drugs by ZIF-8
HOUDINI: A New Approach to Computer-Based Structure Generation
An Extensive and Diverse Set of Molecular Overlays for the Validation of Pharmacophore Programs
Pharmaceutical Perspectives of Nonlinear QSAR Strategies
Molecular Perception for Visualization and Computation: The Proxima Library
Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism
A Database for Large-Scale Docking and Experimental Results
Novel Molecular Representations Using Neumann-Cayley Orthogonal Gated Recurrent Unit
Computer Generation of Molecular Structures by the SMOG Program
CADENCE: Clustering Algorithm─Density-Based Exploration and Novelty Clustering with Efficiency
Rapid evaluation of shape similarity using Gaussian functions
HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention
Long-Distance Structural Consequences of H-Bonding. How H-Bonding Affects Aromaticity of the Ring in Variously Substituted Aniline/Anilinium/Anilide Complexes with Bases and Acids
Comparative Modeling and Benchmarking Data Sets for Human Histone Deacetylases and Sirtuin Families
Properties of Grafted Amphiphilic Chains. A Computer Simulation Study
The Merck Index 13.2 CD-ROM Edition from CambridgeSoft
Local Aromatic Character of C60 and C70 and Their Derivatives
POSIT: Flexible Shape-Guided Docking For Pose Prediction
In Silico Prediction and Biophysical Validation of Novel 14-3-3σ Homodimer Stabilizers
Diagnosing Anorexia Based on Partial Least Squares, Back Propagation Neural Network, and Support Vector Machines
An Iterative Method for Calculation of Group Electronegativities
Drug-Disease Association and Drug-Repositioning Predictions in Complex Diseases Using Causal Inference-Probabilistic Matrix Factorization
Searching for New Leads To Treat Epilepsy: Target-Based Virtual Screening for the Discovery of Anticonvulsant Agents
Compound Classification and Consideration of Correlation with Chemical Descriptors from Articles on Antioxidant Capacity Using Natural Language Processing
Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations
Parallel Screening and Activity Profiling with HIV Protease Inhibitor Pharmacophore Models
QSRR Correlation of Free-Radical Polymerization Chain-Transfer Constants for Styrene
Molecular Topology. 16. Layer Matrixes in Molecular Graphs
Kinase Crystal Miner: A Powerful Approach to Repurposing 3D Hinge Binding Fragments and Its Application to Finding Novel Bruton Tyrosine Kinase Inhibitors
QSAR Analysis of Indole Analogues as Monoamine Oxidase Inhibitors
Building and refining a knowledge base for synthetic organic chemistry via the methodology of inductive and deductive machine learning
Unraveling the Unbinding Pathways of Products Formed in Catalytic Reactions Involved in SIRT1-3: A Random Acceleration Molecular Dynamics Simulation Study
Strategies for Improved Modeling of GPCR-Drug Complexes: Blind Predictions of Serotonin Receptors Bound to Ergotamine
Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations
Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds
Identifying P-Glycoprotein Substrates Using a Support Vector Machine Optimized by a Particle Swarm
On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study
BASIC programs for the evaluation of wavenumbers and for solving polynomials
Applying the constraint satisfaction problem paradigm to structure generation
The Neural Network as a Tool for Multispectral Interpretation
Integrated Knowledge Graph and Drug Molecular Graph Fusion via Adversarial Networks for Drug-Drug Interaction Prediction
The chemical sample: A fundamental object for molecular modeling
tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking
Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts
ABP-Xplorer: A Machine Learning Approach for Prediction of Antibacterial Peptides Targeting Mycobacterium abscessus -tRNA-Methyltransferase (TrmD)
Entrapment of a Weak Polyanion and H + /Na + Exchange in Confined Polyelectrolyte Microcapsules
Modeling Properties with Higher-Level Molecular Connectivity Descriptors
Critical Assessment of Conformal Prediction Methods Applied in Binary Classification Settings
Conformational Sampling of Druglike Molecules with MOE and Catalyst: Implications for Pharmacophore Modeling and Virtual Screening
Comments on "On Bibliometric Analysis of Chinese Research on Cyclization, MALDI-TOF, and Antibiotics: Methodological Concerns"
Molecular Dynamics Flexible Fitting Simulations Identify New Models of the Closed State of the Cystic Fibrosis Transmembrane Conductance Regulator Protein
Structure Prediction of Benzene Clusters Using a Genetic Algorithm
Modeling a Crowdsourced Definition of Molecular Complexity
Inhibition of Aβ 16-22 Peptide Aggregation by Small Molecules and Their Permeation through POPC Lipid Bilayer: Insight from Molecular Dynamics Simulation Study
ChemXTree: A Feature-Enhanced Graph Neural Network-Neural Decision Tree Framework for ADMET Prediction
Molecular Insights into the Trapping Effect of Ca2+ in Protein Kinase A: A Molecular Dynamics Study
Improved and Interpretable Prediction of Cytochrome P450-Mediated Metabolism by Molecule-Level Graph Modeling and Subgraph Information Bottlenecks
Far beyond the structure diagram. Increasing the dimensionality of chemical information retrieval: structure .fwdarw. transport .fwdarw. transformation .fwdarw. energetics .fwdarw. logic and control [networks]
Description of organic reactions based on imaginary transition structures. 9. Single-access perception of rearrangement reactions
Molecular Dynamics Simulations of Complex Mixtures Aimed at the Preparation of Naproxen-Imprinted Xerogels
Molecular Docking with Ligand Attached Water Molecules
Quantum similarity measures, molecular cloud description, and structure-properties relationships
Multivariate Curve Resolution Methods in Imaging Spectroscopy: Influence of Extraction Methods and Instrumental Perturbations
Parallel Random Tunneling Algorithm for Structural Optimization of Lennard-Jones Clusters up to N = 330
Chemical Space and Diversity of the NuBBE Database: A Chemoinformatic Characterization
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids
Topological Indices Based on the Line Graph of the Molecular Graph
ProCite v. 3.4 for Windows and Its NetCite and Biblio-Link Components
AlphaFold-RandomWalk and AlphaFold-Ensemble: Sampling Alternative Protein Conformations with Perturbed Versions of AlphaFold
Combination of Similarity Rankings Using Data Fusion
The AIBLHiCoS Method: Predicting Aqueous p K a Values from Gas-Phase Equilibrium Bond Lengths
Identification of DSC2 as a Key Biomarker for Induction Chemotherapy Sensitivity in Locally Advanced Laryngeal and Hypopharyngeal Squamous Cell Carcinoma
Prediction Accuracy of Production ADMET Models as a Function of Version: Activity Cliffs Rule
Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems
Identification of Novel Disruptor of Telomeric Silencing 1-like (DOT1L) Inhibitors through Structure-Based Virtual Screening and Biological Assays
MultiMCS: A Fast Algorithm for the Maximum Common Substructure Problem on Multiple Molecules
On the Perception of Molecules from 3D Atomic Coordinates
Recent Advances in the Automated Structure Elucidation System, CHEMICS. Utilization of Two-Dimensional NMR Spectral Information and Development of Peripheral Functions for Examination of Candidates
Reliable Model Selection without Reference Values by Utilizing Model Diversity with Prediction Similarity
Parameter-Free Structure-Property Correlation via Progressive Reaction Posets for Substituted Benzenes
An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD
Unlocking the Full Potential of Heteroatom-Doped Graphene-Based Supercapacitors through Stacking Models and SHAP-Guided Optimization
Elucidation of chemical reactivity using an associative memory system
Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems
Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with a Machine Learning Model
Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps
The Chemical Abstracts Service Chemical Registry System. III. Stereochemistry
A New Linear Representation of Chemical Structures
Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases
Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations
Criterion for Evaluating the Predictive Ability of Nonlinear Regression Models without Cross-Validation
Generalizable Framework for Algorithmic Interpretation of Thin Film Morphologies in Scanning Probe Images
In Silico Study of the Radical Scavenging Activities of Natural Indole-3-Carbinols
Investigation of Anti-Alzheimer's Mechanisms of Sarsasapogenin Derivatives by Network-Based Combining Structure-Based Methods
Self-Focusing Virtual Screening with Active Design Space Pruning
Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations
Coupled Anharmonic Thermochemistry from Stratified Monte Carlo Integration
Predicting the Surface Tension of Liquids: Comparison of Four Modeling Approaches and Application to Cosmetic Oils
Simulations of Shikimate Dehydrogenase from Mycobacterium tuberculosis in Complex with 3-Dehydroshikimate and NADPH Suggest Strategies for MtbSDH Inhibition
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations
Chemical information from DIALOG information services
Effect of Cobratoxin Binding on the Normal Mode Vibration within Acetylcholine Binding Protein
ESSESA: An expert system for structure elucidation from spectra. 3. LNSCS for chemical knowledge representation
In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding
Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors
Three-Dimensional QSAR Using the k-Nearest Neighbor Method and Its Interpretation
A Structural Analogue Approach to the Prediction of the Octanol-Water Partition Coefficient
Molecular Insights into the Differential Effects of Acetylation on the Aggregation of Tau Microtubule-Binding Repeats
Enhanced Sampling Reveals Metastable Conformations Driving K417N-Mediated Class I Antibody Escape
Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks
Anatomy of Potency Predictions Focusing on Structural Analogues with Increasing Potency Differences Including Activity Cliffs
GES Polypharmacology Fingerprints: A Novel Approach for Drug Repositioning
TM-search: An Efficient and Effective Tool for Protein Structure Database Search
Pharmacophore Identification, in Silico Screening, and Virtual Library Design for Inhibitors of the Human Factor Xa
Modules Identification in Protein Structures: The Topological and Geometrical Solutions
Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations
High Charge Density in Peptide Dendrimers is Required to Destabilize Membranes: Insights into Endosome Evasion
On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions
Antibody-SGM, a Score-Based Generative Model for Antibody Heavy-Chain Design
Converting chemical formulas to names: an expert strategy
Biophysical Limits of Protein-Ligand Binding
Predicting and Explaining Yields with Machine Learning for Carboxylated Azoles and Beyond
Design of molecules from quantitative structure-activity relationship models. 1. Information transfer between path and vertex degree counts
Novel Treatment of Conformational Flexibility Using Interval Analysis
On a Nonelementary Progress Curve Equation and Its Application in Enzyme Kinetics
Comparison of the Retrieval Effectiveness of CA Condensates (CACon) and CA Subject Index Alert (CASIA)
Contribution of 2D and 3D Structural Features of Drug Molecules in the Prediction of Drug Profile Matching
Combining Free Energy Simulations and NMR Chemical-Shift Perturbation To Identify Transient Cation-π Contacts in Proteins
Baseline Model for Predicting Protein-Ligand Unbinding Kinetics through Machine Learning
A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA
Generalized Fragment-Substructure Based Property Prediction Method
High-Temperature Polymer Dielectrics Designed Using an Invertible Molecular Graph Generative Model
BCT Representation of Chemical Structures
Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction
Computational Validation of the Importance of Absolute Stereochemistry in Virtual Screening
Mathematical Modeling of the Relation between Myosin Phosphorylation and Stress Development in Smooth Muscles
Improved Quantitative Structure Property Relationships for the Prediction of Dielectric Constants for a Set of Diverse Compounds by Subsetting of the Data Set
Predicting Small Molecule Binding Nucleotides in RNA Structures Using RNA Surface Topography
Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship
Interaction of Human β Defensin Type 3 (hBD-3) with Different PIP2-Containing Membranes, a Molecular Dynamics Simulation Study
The Synthesizability of Molecules Proposed by Generative Models
Symantec ACT! 4.0 for Windows
Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations
Hybrid Improved Grey Wolf Support Vector Regression Algorithm for Modeling Solubilities of APIs in Pure Ionic Liquids: σ-Profile Descriptors
Structure-Based Predictions of Activity Cliffs
Lipid Oxidation: Role of Membrane Phase-Separated Domains
On Molecular Polarizability, 4. Evaluation of the Ionization Potential for Alkanes and Alkenes with Polarizability
Molecular Design of Highly Efficient Heavy-Atom-free NpImidazole Derivatives for Two-Photon Photodynamic Therapy and ClO - Detection
An Algorithm for Finding the Smallest Set of Smallest Rings
Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates
Density Functional Theory Transition-State Modeling for the Prediction of Ames Mutagenicity in 1, 4 Michael Acceptors
Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A 2A and A 1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations
Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples
General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps
List operations on chemical graphs. 1. Basic list structures and operations
Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics
Dynamic Electronic Structure Fluctuations in the De Novo Peptide ACC-Dimer Revealed by First-Principles Theory and Machine Learning
Force-Field-Based Computational Study of the Thermodynamics of a Large Set of Aqueous Alkanolamine Solvents for Post-Combustion CO2 Capture
Caffeine Inhibits Tau Aggregation and Destabilizes the Fibril Associated with Chronic Traumatic Encephalopathy: A REST2 and Conventional MD Simulations Study
EViS: An Enhanced Virtual Screening Approach Based on Pocket-Ligand Similarity
Structure-Mutagenicity Study of 12 Trimethylimidazopyridine Isomers Using Orbital Energies and "Spectrum-like Representation" As Descriptors
Tuning Interaction Parameters of Thermoplastic Polyurethanes in a Binary Solvent To Achieve Precise Control over Microphase Separation
ADME Evaluation in Drug Discovery, 6. Can Oral Bioavailability in Humans Be Effectively Predicted by Simple Molecular Property-Based Rules?
IAMPE: NMR-Assisted Computational Prediction of Antimicrobial Peptides
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
Fast evaluation of chemical distance by a simulated-annealing algorithm
From NMR to AI: Do We Need 1 H NMR Experimental Spectra to Obtain High-Quality logD Prediction Models?
Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics
Chemography: Searching for Hidden Treasures
Ligand-Triggered Structural Changes in the M2 Muscarinic Acetylcholine Receptor
The Role of Substituents in Optical Rotation of Oxiranes, Oxetanes, and Oxathietanes
Computer-Aided Molecular Design of Catalysts Based on Mechanism and Structure
A Nomenclature and Structural Representation System for Ladder and Spiro Polymers
A new method of nodal numbering for cyclic and acyclic structures
Novel Variable Selection Quantitative Structure-Property Relationship Approach Based on the k-Nearest-Neighbor Principle
PARM: A Genetic Evolved Algorithm To Predict Bioactivity
LocaPep: Localization of Epitopes on Protein Surfaces Using Peptides from Phage Display Libraries
RICON-The Computer Program for the Quantitative Investigations of Cyclic Organic Molecule Conformations
A Simple Program for Computing Characteristic Polynomials with Mathematica
QUAM-AFM: A Free Database for Molecular Identification by Atomic Force Microscopy
A New Descriptor for Structure-Property and Structure-Activity Correlations