yusuke1997/dblp-id-title huggingface dataset:
Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time
Heterogeneous Catalyst Design Using Stochastic Optimization Algorithms
BILN: A Human-Readable Line Notation for Complex Peptides
Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps
Wiener-Hosoya Index - A Novel Graph Theoretical Molecular Descriptor
MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction
Can One Hear the Shape of a Molecule (from its Coulomb Matrix Eigenvalues)?
Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank
Four-Dimensional Quantitative Structure-Activity Relationship Analysis of a Series of Interphenylene 7-Oxabicycloheptane Oxazole Thromboxane A2 Receptor Antagonists
In Silico Investigation on KAR Signaling Reveals the Significant Dynamic Change of Its Receptor's Structure
Role of Stacking Interactions in the Stability of Primitive Genetics: A Quantum Chemical View
Multistep reactions: the RABBIT approach
Machine-Learning Prediction of Curie Temperature from Chemical Compositions of Ferromagnetic Materials
Influence of Template Size, Canonicalization, and Exclusivity for Retrosynthesis and Reaction Prediction Applications
Identification of Sumoylation Activating Enzyme 1 Inhibitors by Structure-Based Virtual Screening
Where Do We Go from Here on Copyright Impacts and Solutions?
ProBiS-Dock Database: A Web Server and Interactive Web Repository of Small Ligand-Protein Binding Sites for Drug Design
The Use of the Ordered Orthogonalized Multivariate Linear Regression in a Structure-Activity Study of Coumarin and Flavonoid Derivatives as Inhibitors of Aldose Reductase
Protein-Ligand Empirical Interaction Components for Virtual Screening
Structure evaluation using predicted carbon-13 spectra
Computer storage and retrieval of generic chemical structures in patents. 5. Algorithmic generation of fragment descriptors for generic structure screening
Quantitative Structure-Activity Relationship Studies Using Gaussian Processes
SMILES to Smell: Decoding the Structure-Odor Relationship of Chemical Compounds Using the Deep Neural Network Approach
Similarity based on extended basis descriptors
Scaffold-Constrained Molecular Generation
Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions
Topological Shape and Size of Peptides: Identification of Potential Allele Specific Helper T Cell Antigenic Sites
LEADS-PEP: A Benchmark Data Set for Assessment of Peptide Docking Performance
3D Molecular Descriptors Important for Clinical Success
An Atlas of Forecasted Molecular Data. 2. Vibration Frequencies of Main-Group and Transition-Metal Neutral Gas-Phase Diatomic Molecules in the Ground State
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease
A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease
Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets
Extending the Activity Cliff Concept: Structural Categorization of Activity Cliffs and Systematic Identification of Different Types of Cliffs in the ChEMBL Database
The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs
Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language
Multifidelity Neural Network Formulations for Prediction of Reactive Molecular Potential Energy Surfaces
Revealing Comprehensive Food Functionalities and Mechanisms of Action through Machine Learning
Substituent Effects on Thermochemical Properties of C-, N-, O-, and S-Centered Radicals. Physical Interpretation of Substituent Effects
Optimal Molecular Descriptors Based on Weighted Path Numbers
Mechanism of Small Molecules Inhibiting Activator Protein-1 DNA Binding Probed with Induced Fit Docking and Metadynamics Simulations
How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted?
Computational Elucidation of Sterol Recognition by SREBP Cleavage Activatory Protein
The ACS Style Guide. A Manual for Authors and Editors, 2nd ed Edited by Janet S. Dodd. American Chemical Society: Washington, DC, 1997, 460 pp, ISBN 0-8412-3462-0
DeepMPSF: A Deep Learning Network for Predicting General Protein Phosphorylation Sites Based on Multiple Protein Sequence Features
Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor
Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations
Computer-Aided Design and Synthesis of a New Class of PEX14 Inhibitors: Substituted 2, 3, 4, 5-Tetrahydrobenzo[F][1, 4]oxazepines as Potential New Trypanocidal Agents
Identification of Multitarget Activity Ridges in High-Dimensional Bioactivity Spaces
The Retaining Mechanism of Xylose Transfer Catalyzed by Xyloside α-1, 3-Xylosyltransferase (XXYLT1): a Quantum Mechanics/Molecular Mechanics Study
A Robust Neural Network for Extracting Dynamics from Electrostatic Force Microscopy Data
Dissecting Methionine Oxidation by Hydrogen Peroxide in Proteins: Thermodynamics, Kinetics, and Susceptibility Descriptors
Temperature-Dependent Small-Molecule Solubility Prediction Using MoE-Enhanced Directed Message Passing Neural Networks
Enhanced Sampling Simulations of RNA-Peptide Binding Using Deep Learning Collective Variables
The Assembly-Inducing Laulimalide/Peloruside A Binding Site on Tubulin: Molecular Modeling and Biochemical Studies with [ 3 H]Peloruside A
Learning Protein Embedding to Improve Protein Fold Recognition Using Deep Metric Learning
Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein
Virtual Screening of 4-Anilinoquinazoline Analogues as EGFR Kinase Inhibitors: Importance of Hydrogen Bonds in the Evaluation of Poses and Scoring Functions
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)
Retrospect and Prospect of Single Particle Cryo-Electron Microscopy: The Class of Integral Membrane Proteins as an Example
Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods
Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness
General Purpose Interactive Physico-Chemical Property Exploration
Delineation of Agonist Binding to the Human Histamine H 4 Receptor Using Mutational Analysis, Homology Modeling, and ab Initio Calculations
A Computer-Aided Drug Discovery System for Chemistry Teaching
Videoconferencing and Other Distance Education Techniques in Chemoinformatics Teaching and Research at Indiana University
Reciprocal Grids: A Hierarchical Algorithm for Computing Solution X-ray Scattering Curves from Supramolecular Complexes at High Resolution
Use of vector processing to search the Cambridge Structural Database
REACCS in the chemical development environment. 1
Molecular Transformations as a Way of Finding and Exploiting Consistent Local QSAR
Peptide-Aware Chemical Language Model Successfully Predicts Membrane Diffusion of Cyclic Peptides
Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites?
Computer-assisted examination of compounds for common three-dimensional substructures
The Conformational Transitions and Dynamics of Burkholderia cepacia Lipase Regulated by Water-Oil Interfaces
Natural Product-Like Virtual Libraries: Recursive Atom-Based Enumeration
Constructing Optimum Blood Brain Barrier QSAR Models Using a Combination of 4D-Molecular Similarity Measures and Cluster Analysis
Online searching: full text of American Chemical Society primary journals
Estimation of Environment-Related Properties of Chemicals for Design of Sustainable Processes: Development of Group-Contribution + (GC + ) Property Models and Uncertainty Analysis
Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
Protein Secondary Structure Classification Revisited: Processing DSSP Information with PSSC
MDF-DTA: A Multi-Dimensional Fusion Approach for Drug-Target Binding Affinity Prediction
Zigzags, Railroads, and Knots in Fullerenes
Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLC F Antiporter
Graph Theory and Group Contributions in the Estimation of Boiling Points
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6
A Novel Index for the Description of Molecular Linearity
Book Review of The Adobe Illustrator CS Wow! Book (WOW!)
Transition State Searching Accelerated by Neural Network Potential
N-Terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding
Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution
Problem solving with the Beilstein handbook
Mechanistic Model for the Hsp90-Driven Opening of Human Argonaute
Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations
Cassette Dosing Approach and Quantitative Structure-Pharmacokinetic Relationship Study of Antifungal N-Myristoyltransferase Inhibitors
Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads
ProAffinity-GNN: A Novel Approach to Structure-Based Protein-Protein Binding Affinity Prediction via a Curated Data Set and Graph Neural Networks
Refining Drug-Induced Cholestasis Prediction: An Explainable Consensus Model Integrating Chemical and Biological Fingerprints
BatteryBERT: A Pretrained Language Model for Battery Database Enhancement
Quantifying Functional-Group-like Structural Fragments in Molecules and Its Applications in Drug Design
Topological Learning Approach to Characterizing Biological Membranes
Modeling of Ion Complexation and Extraction Using Substructural Molecular Fragments
The CIP System Again: Respecting Hierarchies Is Always a Must
Finite Element Modeling of Atmospheric Water Extraction by Way of Highly Porous Adsorbents: A Roadmap for Solver Construction with Model Factor Sensitivity Screening
Transmembrane β-Barrel Models of α-Synuclein Oligomers
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes
Loop Evolutionary Patterns Shape Catalytic Efficiency of TRI101/201 for Trichothecenes: Insights into Protein-Substrate Interactions
Using Tversky Similarity Searches for Core Hopping: Finding the Needles in the Haystack
Combined Approach Using Ligand Efficiency, Cross-Docking, and Antitarget Hits for Wild-Type and Drug-Resistant Y181C HIV-1 Reverse Transcriptase
Motions of Allosteric and Orthosteric Ligand-Binding Sites in Proteins are Highly Correlated
Insights into Mcl-1 Conformational States and Allosteric Inhibition Mechanism from Molecular Dynamics Simulations, Enhanced Sampling, and Pocket Crosstalk Analysis
Binding of Pollutant Aromatics on Carbon Nanotubes and Graphite
Stability Studies of Transition-Metal Linkage Isomers Using Quantum Mechanical Methods. Groups 11 and 12 Transition Metals
MetalHawk: Enhanced Classification of Metal Coordination Geometries by Artificial Neural Networks
Toxicology information systems: a historical perspective
A Ligand-Based Molecular Modeling Study on Some Matrix Metalloproteinase-1 Inhibitors Using Several 3D QSAR Techniques
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations
Reviews in Computational Chemistry. Edited by Kenny B. Lipkowitz and Donald B. Boyd. VCH Publishers, Volume 6, 1995, xix + 480 pp, ISBN 1-56081-667-8
Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling
Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs?
A Criticism of the Use of Citation Analysis in Studying the Science-Technology Relationship
CAGE: Software for a Critical Analysis of 2H Spin-Lattice Relaxation in Liquid Crystals
DyScore: A Boosting Scoring Method with Dynamic Properties for Identifying True Binders and Nonbinders in Structure-Based Drug Discovery
SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold
EndNote Plus and EndLink 2.0: Database Manager, Bibliography Maker, and Importer of Search Results, New Versions
Cooperative intelligence ecosystems: a proposed design
Computational Fluorine Scanning Using Free-Energy Perturbation
Finite Group Theory for Large Systems. 2. Generating Relations and Irreducible Representations for the Icosahedral Point Group, h
Correction to "Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations"
Structures, Properties, and Dynamics of Intermediates in eEF2-Diphthamide Biosynthesis
Characterizing DNA Origami Nanostructures in TEM Images Using Convolutional Neural Networks
Molecular Modeling and Molecular Dynamics Simulation Studies of the GSK3β/ATP/Substrate Complex: Understanding the Unique P+4 Primed Phosphorylation Specificity for GSK3β Substrates
A Substructural Analysis Method for Structure-Activity Correlation of Heterocyclic Compounds Using Wiswesser Line Notation
UTAB: a computer database on residues of xenobiotic organic chemicals and heavy metals in plants
Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction
Effective Descriptions of Molecular Structures and the Quantitative Structure-Activity Relationship Studies
An oxidation number assignment expert for CHEMPROF
Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking
Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells
DGSS: A Dynamic Interaction Graph Neural Network with Specific Substructure Awareness for Drug Synergy Prediction
Protein Structural Model Selection Informed by Comparison of Predicted Ligand Binding Poses
Intuition-Enabled Machine Learning Beats the Competition When Joint Human-Robot Teams Perform Inorganic Chemical Experiments
Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions Approaches
Improving DNA 6mA Site Prediction via Integrating Bidirectional Long Short-Term Memory, Convolutional Neural Network, and Self-Attention Mechanism
Automated Recycling of Chemistry for Virtual Screening and Library Design
Assessing How Well a Modeling Protocol Captures a Structure-Activity Landscape
HAD: An Automated Database Tool for Analyzing Screening Hits in Drug Discovery
Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra Using Genetic Algorithms and Neural Networks
Structural Characterizations of Oligopyridyl Foldamers, α-Helix Mimetics
The Computer-Based Chemical Structure Information System of Merck Sharp and Dohme Research Laboratories
INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool
Particle Mass Ratios and Similar Volumetric Ratios in Geometry
Molecular Dynamics Simulations and Diversity Selection by Extended Continuous Similarity Indices
An Automated Approach for Domain-Specific Knowledge Graph Generation─Graph Measures and Characterization
Assessment of Molecular Similarity from the Analysis of Randomly Generated Structural Fragment Populations
Investigating Errors in Alchemical Free Energy Predictions Using Random Forest Models and GaMD
Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins
Probing the Functional Topology of a pH-Dependent Triple Helix DNA Nanoswitch Family through Gaussian Accelerated MD Simulation
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches
Can Current Molecular Docking Methods Accurately Predict RNA Inhibitors?
Chemical Information Based Scaling of Molecular Descriptors: A Universal Chemical Scale for Library Design and Analysis
Yet Another Representation of Molecular Structure
ChipCheck-A Program Predicting Total Hybridization Equilibria for DNA Binding to Small Oligonucleotide Microarrays
Chemistry Meets Biology: Cross-Disciplinary Evaluation of Drug Discovery Databases
Breaking the Barriers: Machine-Learning-Based c-RASAR Approach for Accurate Blood-Brain Barrier Permeability Prediction
Bioactivity Deep Learning for Complex Structure-Free Compound-Protein Interaction Prediction
Substructure search systems. 1. Performance comparison of the MACCS, DARC, HTSS, CAS Registry MVSSS, and S4 substructure search systems
String Kernels and High-Quality Data Set for Improved Prediction of Kinked Helices in α-Helical Membrane Proteins
A new system for the designation of chemical compounds. 1. Theoretical preliminaries and the coding of acyclic compounds
Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β42
A Twist of Fate: The Helix-Turn-Helix Motif in Pseudomonas aeruginosa ExsA Can Allosterically Stabilize the Ligand-Binding Domain
The numbers of structural isomers, stereoisomers, and chiral and achiral stereoisomers of fluorochloroalkanes
Meta-Analysis and Topological Perturbation in Interactomic Network for Antiopioid Addiction Drug Repurposing
Interference of Boswellic Acids with the Ligand Binding Domain of the Glucocorticoid Receptor
SH2 Binding Site Comparison: A New Application of the SURFCOMP Method
LigMate: A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening
Impact of Chemist-In-The-Loop Molecular Representations on Machine Learning Outcomes
Accommodating Statistical and Physics-Based Computational Protocols for Molecular Glue Model and Evaluation
Toward a Computational NMR Procedure for Modeling Dipeptide Side-Chain Conformation
Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application
ChemWindow DB (4.0)
A Criteria To Classify Biological Activity of Benzimidazoles from a Model of Structural Similarity
Automatic Spectra Interpretation, Structure Generation, and Ranking
A combined model-building and distance-geometry approach to automated conformational analysis and search
Integration of Ligand Field Molecular Mechanics in Tinker
Heuristic refinement method for the derivation of protein solution structures: validation on cytochrome b562
Recursive Random Forests Enable Better Predictive Performance and Model Interpretation than Variable Selection by LASSO
Framework for Inverse Mapping Chemistry-Agnostic Coarse-Grained Simulation Models into Chemistry-Specific Models
Quantum Machine Learning Predicting ADME-Tox Properties in Drug Discovery
Engineering Protein Dynamics through Mutational Energy Landscape Traps
Evaluation and implementation of topological codes for online compound search and registration
Predicting p K a
Comments on "Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets": Significance for the Validation of Scoring Functions
Generative Models for Chemical Structures
SMILES Token Additivity Model with Interpretability and Generalizability for Fuel Property Predictions
Molecular Determinants for the Activation/Inhibition of Bak Protein by BH3 Peptides
The Use of Robust Smoothers in Nuclear Material Safeguards
Efficiently Transplanting Potential Energy Interpolation Database between Two Systems: Bacteriochlorophyll Case with FMO and LH2 Complexes
SPECTRA: A Spectral Information Management System Featuring a Novel Combined Search Function
Improved Structure-Based Histidine p K a Prediction for pH-Responsive Protein Design
MOFGPT: Generative Design of Metal-Organic Frameworks using Language Models
Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data
Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides
Scientific communication pathways: an overview and introduction to a symposium
Extraction of Data on Parent Compounds and Their Metabolites from Texts of Scientific Abstracts
Cyclic Peptides as Protein Kinase Inhibitors: Structure-Activity Relationship and Molecular Modeling
Molecular Mechanism of Selective Binding of Peptides to Silicon Surface
Large Virtual Enhancement of a 13C NMR Database. A Structural Crowning Extrapolation Method Enabling Spectral Data Transfer
Accurate VLE Predictions via COSMO-RS-Guided Deep Learning Models: Solubility and Selectivity in Physical Solvent Systems for Carbon Capture
Insights into the Molecular Inhibition of the Oncogenic Channel KV10.1 by Globular Toxins
Free Energy Coupling between DNA Bending and Base Flipping
QSAR Classification Model for Antibacterial Compounds and Its Use in Virtual Screening
User needs in chemical information
Correction to "Development of a Pantetheine Force Field Library for Molecular Modeling"
Compound Pathway Model To Capture SAR Progression: Comparison of Activity Cliff-Dependent and -Independent Pathways
Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots
Visual Characterization and Diversity Quantification of Chemical Libraries: 2. Analysis and Selection of Size-Independent, Subspace-Specific Diversity Indices
LS-MolGen: Ligand-and-Structure Dual-Driven Deep Reinforcement Learning for Target-Specific Molecular Generation Improves Binding Affinity and Novelty
Generalization of a Targeted Library Design Protocol: Application to 5-HT 7 Receptor Ligands
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion
3D QSAR and Molecular Docking Studies of Benzimidazole Derivatives as Hepatitis C Virus NS5B Polymerase Inhibitors
Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces
PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules Using B3LYP/6-31G* Calculations
Analysis and Study of Molecule Data Sets Using Snowflake Diagrams of Weighted Maximum Common Subgraph Trees
Prediction of Aqueous Solubility of Organic Compounds from Molecular Structure
Hyperstructure model for chemical structure handling: Techniques for substructure searching
Characterizing the Strength of Individual Hydrogen Bonds in DNA Base Pairs
PATTY: A programmable atom type and language for automatic classification of atoms in molecular databases
Comments on the Definition of the Q 2 Parameter for QSAR Validation
Machine Learning Consensus To Predict the Binding to the Androgen Receptor within the CoMPARA Project
What Do We Know about C 28 H 14 and C 30 H 14 Benzenoid Hydrocarbons and Their Evolution to Related Polymer Strips?
Virtual Compound Libraries in Computer-Assisted Drug Discovery
QSAR Study of Catalytic Asymmetric Reactions with Topological Indices
Maximum Common Substructure-Based Data Fusion in Similarity Searching
Quantitative Structure-Activity Relationship Models for Ready Biodegradability of Chemicals
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors
Analysis of Permanent Electric Dipole Moments of Aliphatic Hydrocarbon Molecules. 2. DFT Results
Neural Message Passing for NMR Chemical Shift Prediction
Long-Range Strategies in the LHASA Program: The Quinone Diels-Alder Transform
Modeling the Interface between Islet Amyloid Polypeptide and Insulin-Based Aggregation Inhibitors: Correlation to Aggregation Kinetics and Membrane Damage
Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein
A Study of Structure-Carcinogenic Potency Relationship with Artificial Neural Networks. The Using of Descriptors Related to Geometrical and Electronic Structures
Mechanism of Selective Aromatic Hydroxylation in the Metabolic Transformation of Paclitaxel Catalyzed by Human CYP3A4
Crossfile Searching with QPAT-US Using WordBasic Macro Tools
Deep-Learning-Based End-to-End Predictions of CO 2 Capture in Metal-Organic Frameworks