yusuke1997/dblp-id-title huggingface dataset:
DIVSEL and COMPLIB - Strategies for the Design and Comparison of Combinatorial Libraries using Pharmacophoric Descriptors
DeepKa Web Server: High-Throughput Protein p K a Prediction
Entropy of Proteins Using Multiscale Cell Correlation
Theoretical Prediction of Hydrogen Bond Strength for Use in Molecular Modeling
Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity
Improved Naïve Bayesian Modeling of Numerical Data for Absorption, Distribution, Metabolism and Excretion (ADME) Property Prediction
Polypharmacology Directed Compound Data Mining: Identification of Promiscuous Chemotypes with Different Activity Profiles and Comparison to Approved Drugs
Dense Neural Network for Calculating Solvation Free Energies from Electronegativity-Equalization Atomic Charges
Application of Symmetry Functions to Large Chemical Spaces Using a Convolutional Neural Network
Structure-Activity Relationships and Anti-inflammatory Activities of N -Carbamothioylformamide Analogues as MIF Tautomerase Inhibitors
Need for Cross-Validation of Single Particle Cryo-EM
How Good are Current Pocket-Based 3D Generative Models?: The Benchmark Set and Evaluation of Protein Pocket-Based 3D Molecular Generative Models
Advancements in Ligand-Based Virtual Screening through the Synergistic Integration of Graph Neural Networks and Expert-Crafted Descriptors
Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds
Prediction of Inhibitory Activity against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models
QSAR of Flavylium Salts as Inhibitors of Xanthine Oxidase
Atomic Polarizabilities for Interactive Dipole Induction Models
Graph theoretical algorithm to canonically name the isomers of the regular polyhedranes
Letters to the Editor-BIBLIOMETRICS AND DRUGS
A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication
Probing the Structural and Electronic Factors Affecting the Adsorption and Reactivity of Alkenes in Acidic Zeolites Using DFT Calculations and Multivariate Statistical Methods
ConSystant and Chemeleon
Wolf 2 Pack - Portal Based Atomistic Force-Field Development
Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level
Generic structure storage and retrieval
Iterative Regression of Corrective Baselines (IRCB): A New Model for Quantitative Spectroscopy
Spectroscopic QSAR Methods and Self-Organizing Molecular Field Analysis for Relating Molecular Structure and Estrogenic Activity
Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics
Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery
DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening
Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems
Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation
Determination of McGowan Volumes for Ions and Correlation with van der Waals Volumes
Research Progresses and Applications of Knowledge Graph Embedding Technique in Chemistry
A New Topological Index for QSPR of Alkanes
WinDat: An NMR Database Compilation Tool, User Interface, and Spectrum Libraries for Personal Computers
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions
Spectrophotometric Determination and Computational Evaluation of the Rates of Hydrolysis of 9-Amino-Substituted Acridines
Stochastic Generator of Chemical Structure. 1. Application to the Structure Elucidation of Large Molecules
Recursive Median Partitioning for Virtual Screening of Large Databases
Data Mining a Small Molecule Drug Screening Representative Subset from NIH PubChem
Ab Initio vs Molecular Mechanics Thermochemistry: Homocubanes
Unique Physicochemical Patterns of Residues in Protein-Protein Interfaces
Atlasing of Assembly Landscapes using Distance Geometry and Graph Rigidity
Voice-operated microcomputer-based laboratory data acquisition system to aid handicapped students in chemistry laboratories
Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures
E-State Modeling of Corticosteroids Binding AffinityValidation of Model for Small Data Set
Conformer Generation for Structure-Based Drug Design: How Many and How Good?
Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks
Elucidating Hyperconjugation from Electronegativity to Predict Drug Conformational Energy in a High Throughput Manner
Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies
ASVirus: A Comprehensive Knowledgebase for the Viral Alternative Splicing
Data Fusion of Similarity and Dissimilarity Measurements Using Wiener-Based Indices for the Prediction of the NPY Y5 Receptor Antagonist Capacity of Benzoxazinones
IUCLID: An Information Management Tool for Existing Chemicals and Biocides
Evaluation of the ABCG2 Charge Model in Protein-Ligand Binding Free-Energy Calculations
Dense Graphs and Sparse Matrices
Homology Model-Based Virtual Screening for the Identification of Human Helicase DDX3 Inhibitors
ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design
IntEnzyDB: an Integrated Structure-Kinetics Enzymology Database
MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations
Active Learning with Support Vector Machine Applied to Gene Expression Data for Cancer Classification
Some Bounds for the Connectivity Index of a Chemical Graph
Searching Chemical Space with the Bayesian Idea Generator
Golden Anniversary of the ACS Division of Chemical Information (1948-1998)
Increasing the Coverage of Medicinal Chemistry-Relevant Space in Commercial Fragments Screening
Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase
Analysis of Conformational Coverage, 1. Validation and Estimation of Coverage
Computational Prediction of a New ADMET Endpoint for Small Molecules: Anticommensal Effect on Human Gut Microbiota
Refinement and Use of the Approximate Similarity in QSAR Models for Benzodiazepine Receptor Ligands
Minimum Energy Pathway for Lesion Recognition and DNA Binding by RAD4/XPC
High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data
Receptor- and Ligand-Based Study on Novel 2, 2′-Bithienyl Derivatives as Non-Peptidic AANAT Inhibitors
Unconventional Plasticity of HIV-1 Reverse Transcriptase: How Inhibitors Could Open a Connection "Gate" between Allosteric and Catalytic Sites
PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser
Asymmetric Dynamics Between the Protomers of the σ2 Receptor Homodimer
Theoretical Prediction of Hydrogen-Bond Basicity p K BHX Using Quantum Chemical Topology Descriptors
Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop
The Chemical Abstracts Service generic chemical (Markush) structure storage and retrieval capability. 2. The MARPAT file
Molecular Geometry as a Source of Chemical Information. 5. Substituent Effect on Proton Transfer in Para-Substituted Phenol Complexes with Fluoride-a B3LYP/6-311+G** Study
KNDM: A Knowledge Graph Transformer and Node Category Sensitive Contrastive Learning Model for Drug and Microbe Association Prediction
Virtual Decoy Sets for Molecular Docking Benchmarks
A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes
A combined model of multi-resonance subspectra/substructure and DARC topological structure representation. Local and global knowledge in the carbon-13 NMR DARC database
Qualitative Estimation of Protein-Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations
Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis
Crowdsourcing Yields a New Standard for Kinks in Protein Helices
Lipophilicity of Coarse-Grained Cholesterol Models
Exploring QSAR. By Corwin Hansch, Albert Leo, and David Hoekman. American Chemical Society, Washington, DC, 1995, 2 Vols
Basis Set Exchange: A Community Database for Computational Sciences
Fullerenes as Tilings of Surfaces
A computer program for generation of constitutionally isomeric structural formulas
CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup and Local Rotational Symmetry Consideration
PUCHIK: A Python Package To Analyze Molecular Dynamics Simulations of Aspherical Nanoparticles
Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation
Cluster-MLP: An Active Learning Genetic Algorithm Framework for Accelerated Discovery of Global Minimum Configurations of Pure and Alloyed Nanoclusters
Quantifying the Relationships among Drug Classes
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands
Computer storage and retrieval of generic chemical structures in patents. 6. An interpreter program for the generic structure description language GENSAL
Use of Automatic Relevance Determination in QSAR Studies Using Bayesian Neural Networks
Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling
Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries
Comparative efficiency of searching abstract text in the Chemical Abstracts Service database
Classification of Compounds with Distinct or Overlapping Multi-Target Activities and Diverse Molecular Mechanisms Using Emerging Chemical Patterns
Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor
Adaptative Steered Molecular Dynamics Study of Mutagenesis Effects on Calcium Affinity in the Regulatory Domain of Cardiac Troponin C
Parameter Choice Matters: Validating Probe Parameters for Use in Mixed-Solvent Simulations
Invariant Molecular Representations for Heterogeneous Catalysis
RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases
Chemical symbol string parser
Application of pattern recognition techniques to mass spectrometric data for sequencing C-terminal peptide residue series
Assessment of a Cambridge Structural Database-Driven Overlay Program
Modeling Robust QSAR. 1. Coding Molecules in 3D-QSAR - from a Point to Surface Sectors and Molecular Volumes
CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design
Extensions to the STAR File Syntax
Structural Similarity Based Kriging for Quantitative Structure Activity and Property Relationship Modeling
An Interactive Substructure Search System
Effects of Metal Ions on Aβ42 Peptide Conformations from Molecular Simulation Studies
Calculation of Substructural Analysis Weights Using a Genetic Algorithm
DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines
QSAR in Ecotoxicity: An Overview of Modern Classification Techniques
RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries
Method for estimating the human and environmental exposure potential of chemicals having designated uses
Discovery of New Inhibitors of Mycobacterium tuberculosis InhA Enzyme Using Virtual Screening and a 3D-Pharmacophore-Based Approach
Response to the Comment on "Exhaustive Generation of Organic Isomers. 5. Unsaturated Optical and Geometrical Stereoisomers and a New CIP Subrule"
A versatile, efficient, and interactive program to build molecular structures for theoretical calculations and chemical information system
A Novel Method for Building Regression Tree Models for QSAR Based on Artificial Ant Colony Systems
Unraveling the Abnormal Molecular Mechanism of Suicide Inhibition of Cytochrome P450 3A4
Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?
Prediction of Thermodynamic Parameters in Gas Chromatography from Molecular Structure: Hydrocarbons
TIDAL: Topology-Inferred Drug Addiction Learning
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions
PLA-MoRe: A Protein-Ligand Binding Affinity Prediction Model via Comprehensive Molecular Representations
Enhancing Monte Carlo Tree Search for Retrosynthesis
Leveraging Transfer Learning and Chemical Principles toward Interpretable Materials Properties
Multirelational Hypergraph Representation Learning for Predicting circRNA-miRNA Associations
Computerized Stereochemistry: Coding and Naming Configurational Stereoisomers
A Cellular Automata Model of Bond Interactions Among Molecules
Unified Model to Predict gRNA Efficiency across Diverse Cell Lines and CRISPR-Cas9 Systems
Quantitative Structure-Property Relationships (QSPRs) for the Estimation of Vapor Pressure: A Hierarchical Approach Using Mathematical Structural Descriptors
PythoMS: A Python Framework To Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins
Autocorrelation Method Adapted To Generate New Atomic Environments: Application for the Prediction of 13-C Chemical Shifts of Alkanes
ESSESA: An expert system for structure elucidation from spectra, 6. Substructure constraints from analysis of 13C-NMR spectra
The Value of Peer Mentoring Networks for Developing Leaders and Inspiring Change
Comparative Molecular Field Analysis Using Molecular Integral Equation Theory
PDFDataExtractor: A Tool for Reading Scientific Text and Interpreting Metadata from the Typeset Literature in the Portable Document Format
Context-Based Features Enhance Protein Secondary Structure Prediction Accuracy
Similarity Searching in Files of Three-Dimensional Chemical Structures. Alignment of Molecular Electrostatic Potential Fields with a Genetic Algorithm
Comment on "Exhaustive Generation of Organic Isomers, 5. Unsaturated Optical and Geometrical Stereoisomers and a New CIP Subrule"
Consensus Prediction of Human Gut Microbiota-Mediated Metabolism Susceptibility for Small Molecules by Machine Learning, Structural Alerts, and Dietary Compounds-Based Average Similarity Methods
Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches
Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosis DNA Gyrase ATPase Activity
Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling
Difference and Influence of Inactive and Active States of Cannabinoid Receptor Subtype CB2: From Conformation to Drug Discovery
Algorithm for Efficient Superposition and Clustering of Molecular Assemblies Using the Branch-and-Bound Method
A Simple Approach for Indexing the Oral Druglikeness of a Compound: Discriminating Druglike Compounds from Nondruglike Ones
Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation
New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community
All-Atom Simulations Reveal the Effect of Membrane Composition on the Signaling of the NKG2A/CD94/HLA-E Immune Receptor Complex
Quantum Pharmacological Analysis of Structure-Activity Relationships for Mefloquine Antimalarial Drugs Using Optimal Transformations
Attempting Well-Tempered Funnel Metadynamics Simulations for the Evaluation of the Binding Kinetics of Methionine Aminopeptidase-II Inhibitors
Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design
Past Perfect, Present Perfect, Future Perfect-Quality Assessment and Quality Control Mechanisms at Beilstein
Introduction of an Information-Theoretic Method to Predict Recovery Rates of Active Compounds for Bayesian in Silico Screening: Theory and Screening Trials
Predicting Antimicrobial Peptides Using ESMFold-Predicted Structures and ESM-2-Based Amino Acid Features with Graph Deep Learning
Conformational Coverage by a Genetic Algorithm
Formulation of isomeric reaction types and systematic enumeration of six-electron pericyclic reactions
Computer storage and retrieval of generic structures in chemical patents. 4. An extended connection table representation for generic structures
Insight into the Fundamental Interactions between LEDGF Binding Site Inhibitors and Integrase Combining Docking and Molecular Dynamics Simulations
Sensitivity Analysis and Other Improvements to Tailored Combinatorial Library Design
Data Evaluation in High-Performance Liquid Chromatography-Diode-Array Detection-Fluorescence Detection by Information Theory
LGGA-MPP: Local Geometry-Guided Graph Attention for Molecular Property Prediction
MetalloGen: Automated 3D Conformer Generation for Diverse Coordination Complexes
Toward a Better Pharmacophore Description of P-Glycoprotein Modulators, Based on Macrocyclic Diterpenes from Euphorbia Species
Facile Solutions to the Problems Associated with Chemical Information and Mathematical Symbolism While Using Machine Translation Tools
Prediction of Chemical Carcinogenicity from Molecular Structure
Computer Generation of Automorphism Groups of Weighted Graphs
Comparative Studies on Some Metrics for External Validation of QSPR Models
Molecular Mechanism-Driven Discovery of Novel Small Molecule Inhibitors against Drug-Resistant SARS-CoV-2 M pro Variants
GPCR Structure-Based Virtual Screening Approach for CB2 Antagonist Search
Consensus Methods for Combining Multiple Clusterings of Chemical Structures
Computer Editing of General Subject Heading Data for Chemical Abstracts Volume Indexes
Critical Residue That Promotes Protein Dimerization: A Story of Partially Exposed Phe 25 in 14-3-3σ
Determination of Toxicant Mode of Action by Augmented Top Priority Fragment Class
Principle for Exhaustive Enumeration of Unique Structures Consistent with Structural Information
Protein-Ligand Scoring with Convolutional Neural Networks
Convergence of Atomic Charges with the Size of the Enzymatic Environment
Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular Dynamics
Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning
Prediction of Chromatographic Retention Time of a Small Molecule from SMILES Representation Using a Hybrid Transformer-LSTM Model
Can 'Bacterial-Metabolite-Likeness' Model Improve Odds of 'in Silico' Antibiotic Discovery?
Artificial Intelligence Agents for Materials Sciences
Applications of Systematic Molecular Scaffold Enumeration to Enrich Structure-Activity Relationship Information
MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction
Free Energy Perturbation Simulations Measure the Change in Binding Affinity of the Aβ25-35 Peptide to the Zwitterionic Bilayer Caused by Oxidation
Ab Initio Study of Chlorosilanes: Dipole Moments and Charge Distributions
Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations
Computational Simulations of the Interactions between Acetyl-Coenzyme-A Carboxylase and Clodinafop: Resistance Mechanism Due to Active and Nonactive Site Mutations
Estimation of Ligand Binding Free Energy Using Multi-eGO
Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein-Ligand Complexes using ab Initio Calculations
Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study
Support Vector Machines for the Estimation of Aqueous Solubility
Distinguishing between Bioactive and Modeled Compound Conformations through Mining of Emerging Chemical Patterns
Application of high-resolution computer graphics to pattern recognition analysis
Disentangling the Contribution of Each Descriptive Characteristic of Every Single Mutation to Its Functional Effects
Topological organic chemistry. 7. Graph theory and molecular topological indexes of unsaturated and aromatic hydrocarbons
Gradual in Silico Filtering for Druglike Substances
Unbinding Pathways of VEGFR2 Inhibitors Revealed by Steered Molecular Dynamics
From NMR to AI: Designing a Novel Chemical Representation to Enhance Machine Learning Predictions of Physicochemical Properties
Computational Prediction and Validation of an Expert's Evaluation of Chemical Probes
Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET
Investigation of Infrared Spectra-Structure Correlation Using Kohonen and Counterpropagation Neural Network
Enhancing Chemical Reaction Monitoring with a Deep Learning Model for NMR Spectra Image Matching to Target Compounds
Specialized Reference Works and Their Users. A Preliminary Study
Quantum Similarity Superposition Algorithm (QSSA): A Consistent Scheme for Molecular Alignment and Molecular Similarity Based on Quantum Chemistry
ChemSem: An Extensible and Scalable RSS-Based Seminar Alerting System for Scientific Collaboration
Partner-Specific Prediction of Protein-Dimer Stability from Unbound Structure of Monomer
Enhancing Coarse-Grained Models through Machine Learning
ReLMM: Reinforcement Learning Optimizes Feature Selection in Modeling Materials
Prediction of Thermogravimetric Data in Bromine Captured from Brominated Flame Retardants (BFRs) in e-Waste Treatment Using Machine Learning Approaches
A Graph-Based Machine Learning Framework for Predicting Physicochemical Properties of Antiviral Drugs via Topological Indices
Prediction of Natural Product Classes Using Machine Learning and 13C NMR Spectroscopic Data
Discovery of a New Donepezil-like Acetylcholinesterase Inhibitor for Targeting Alzheimer's Disease: Computational Studies with Biological Validation
Modeling Molecularly Imprinted Nanoparticles with LNKD: A Resource Efficient Algorithm for Polymer Cross-Linking
DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules
KGG : Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions
Characterization of a Novel Monoclonal Antibody with High Affinity and Specificity against Aflatoxins: A Discovery from Rosetta Antibody-Ligand Computational Simulation
QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets
STN Express
Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers
Benchmarking Zinc-Binding Site Predictors: A Comparative Analysis of Structure-Based Approaches
Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability
The Extent of the Relationship between the Graph-Theoretical and the Geometrical Shape Coefficients of Chemical Compounds
Kekule: OCR-optical chemical (structure) recognition
Atomistic Molecular Insights into Angiotensin-(1-7) Interpeptide Interactions
Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field
The Laplacian matrix in chemistry
Identification of Common Functional Configurations Among Molecules
Adsorption Energy Prediction Model for CO 2 Reduction on Electrocatalysts Containing Previously Unencountered Metal Elements
Bit-String Methods for Selective Compound Acquisition
Assessment of Machine Learning Reliability Methods for Quantifying the Applicability Domain of QSAR Regression Models
Structure-Based CoMFA As a Predictive Model - CYP2C9 Inhibitors As a Test Case