yusuke1997/dblp-id-title huggingface dataset:
CoNTub v2.0 - Algorithms for Constructing C 3 -Symmetric Models of Three-Nanotube Junctions
Web-Based Tools for Mining the NCI Databases for Anticancer Drug Discovery
Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis
Application of the Genetic Algorithm Joint with the Powell Method to Nonlinear Least-Squares Fitting of Powder EPR Spectra
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks
Uniparametricity-Why a Canonical Ordering (and a Consistent Nomenclature) for Organic Compounds Continues To Evade Us
Hybrid Structure-Based Virtual Screening Protocol for the Identification of Novel BACE1 Inhibitors
The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors
In Silico Modeling of PROTAC-Mediated Ternary Complexes: Validation and Application
Fuzzy ARTMAP and Back-Propagation Neural Networks Based Quantitative Structure-Property Relationships (QSPRs) for Octanol-Water Partition Coefficient of Organic Compounds
New index for clustering tendency and its application to chemical problems
Atomic-Level-Based AI Topological Descriptors for Structure-Property Correlations
LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening
New Molecular Descriptors Based on Local Properties at the Molecular Surface and a Boiling-Point Model Derived from Them
Application of automated structure analysis to some organic compounds using PCs. 1. Automated Patterson techniques
AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets
Genetic Algorithm Applied to the Selection of Factors in Principal Component-Artificial Neural Networks: Application to QSAR Study of Calcium Channel Antagonist Activity of 1, 4-Dihydropyridines (Nifedipine Analogous)
Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion's Polarizability and Molecular Mass with Limited Data
Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function
Persistent Path-Spectral (PPS) Based Machine Learning for Protein-Ligand Binding Affinity Prediction
Design and Evaluation of a Novel Class-Directed 2D Fingerprint to Search for Structurally Diverse Active Compounds
Duplications among Reaction Databases
Predicting Drug-Drug Interaction via Dual-Drug Visual Representation
ALC: Active Library on Corrosion
Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein-Ligand Interactions
SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions
Quality Criteria of Genetic Algorithms for Structure Optimization
Improvement of Virtual Screening Results by Docking Data Feature Analysis
QM/MM Simulations of Amyloid-β 42 Degradation by IDE in the Presence and Absence of ATP
Protein Flexibility in Virtual Screening: The BACE-1 Case Study
Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program
Integrating Drug's Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury
An Algorithm-Based Investigation to Reveal the Differential Dynamics of Water inside Protein Cavities as a Function of Distance from Their Wall
Copyright Impacts on Chemical-Industry Users and Information Centers
Topological torsion: a new molecular descriptor for SAR applications. Comparison with other descriptors
In Silico Structural Modeling of the HuR-mRNA Complex: Insights into Structural and Functional Regulation
De N ovo -Designed Miniprotein Inhibits the Enzymatic Activity of the SARS-CoV-2 Main Protease
MOSAIC: A Data Model and File Formats for Molecular Simulations
The PHARMSEARCH database
A Novel Formalism To Characterize the Degree of Unsaturation of Organic Molecules
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale
CO 2 -Formatics: How Do Proteins Bind Carbon Dioxide?
Chemical Registries-in the Fourth Decade of Service
XenoNet: Inference and Likelihood of Intermediate Metabolite Formation
Application of Free Energy Perturbation for the Design of BACE1 Inhibitors
SPROUT: Recent developments in the de novo design of molecules
Sixth International Conference on Mathematical Chemistry
Low-Cost, High-Accuracy Reactivity Modeling: Integrating Genetic Algorithms and Machine Learning with Multilevel DFT Calculations
Compound Activity Prediction with Dose-Dependent Transcriptomic Profiles and Deep Learning
Structure generation of constitutional isomers from structural fragments
Andrographolide: A Diterpenoid from Cymbopogon schoenanthus Identified as a New Hit Compound against Trypanosoma cruzi Using Machine Learning and Experimental Approaches
Locating Biologically Active Compounds in Medium-Sized Heterogeneous Datasets by Topological Autocorrelation Vectors: Dopamine and Benzodiazepine Agonists
Molecular Similarity Analysis and Virtual Screening by Mapping of Consensus Positions in Binary-Transformed Chemical Descriptor Spaces with Variable Dimensionality
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations
CASREACT: more than a million reactions
Machine Learning-Driven Prediction of Electrochemical Promotion in the Reverse Water Gas Shift Reaction
ALFA: Automatic Ligand Flexibility Assignment
External Validation and Prediction Employing the Predictive Squared Correlation Coefficient Test Set Activity Mean vs Training Set Activity Mean
mkgridXf: Consistent Identification of Plausible Binding Sites Despite the Elusive Nature of Cavities and Grooves in Protein Dynamics
iScore: A ML-Based Scoring Function for De Novo Drug Discovery
Improved Estimation of the Ranking Probabilities in Partial Orders Using Random Linear Extensions by Approximation of the Mutual Ranking Probability
Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking
Topological Analysis of Long-Chain Branching Patterns in Polyolefins
SCISSORS: Practical Considerations
Unveiling the Atomic-Level Determinants of Acylase-Ligand Complexes: An Experimental and Computational Study
ProtoCaller: Robust Automation of Binding Free Energy Calculations
Deep Learning for Drug-Induced Liver Injury
Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network
OmniCLIC: A Unified Omics Contrastive Learning Framework for Effective Integration and Classification of Multiomics Data
FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity
On Molecular Polarizability: 2. Relationship to the Boiling Point of Alkanes and Alcohols
In silico Comparison of Antimycobacterial Natural Products with Known Antituberculosis Drugs
Computerized chemical structure-handling techniques in structure-activity studies and molecular property prediction
Deep Learning Models for Predicting Human Cytochrome P450 Inhibition and Induction
Mass Spectrometry Adduct Calculator
Evaluating the Multifunctionality of a New Modulator of Zinc-Induced Aβ Aggregation Using a Novel Computational Approach
Improving Docking Power for Short Peptides Using Random Forest
Pro-Search, Pro-Cite, and Biblio-Links
Representing Clusters Using a Maximum Common Edge Substructure Algorithm Applied to Reduced Graphs and Molecular Graphs
Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study
Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models
Data-Driven Optimization of Industrial Impact Polypropylene Characterization: Machine Learning Insights
Targeting Self-Binding Peptides as a Novel Strategy To Regulate Protein Activity and Function: A Case Study on the Proto-oncogene Tyrosine Protein Kinase c -Src
Ab Initio Simulations and Materials Chemistry in the Age of Big Data
Explainable Graph Neural Networks in Chemistry: Combining Attribution and Uncertainty Quantification
Design of Diverse and Focused Combinatorial Libraries Using an Alternating Algorithm
Prediction of the Dissociation Constant p K a of Organic Acids from Local Molecular Parameters of Their Electronic Ground State
The Effect of Surface Composition on the Selective Capture of Atmospheric CO 2 by ZIF Nanoparticles: The Case of ZIF-8
Mapping Context-Aware Phosphosite Regulation of Protein-Protein Interactions Using Deep Learning and Pan-Cancer Proteomics
Strategic Design of Fluorescent Perylene-Modified Nucleic Acid Monomers: Position-, Phosphorylation-, and Linker-Dependent Control of Electron Transfer
Equivariant Graph-Representation-Based Actor-Critic Reinforcement Learning for Nanoparticle Design
QSAR Analyses of Skin Penetration Enhancers
Computational Multitarget Drug Design
AlphaFold2 Predicts Whether Proteins Interact Amidst Confounding Structural Compatibility
Machine Learning on DNA-Encoded Library Count Data Using an Uncertainty-Aware Probabilistic Loss Function
BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation
Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning
Dehydration Determines Hydrotropic Ion Affinity for Zwitterionic Micelles
Quantitative Structure-Property Relationship (QSPR) Correlation of Glass Transition Temperatures of High Molecular Weight Polymers
GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations
Assessing Synthetic Accessibility of Chemical Compounds Using Machine Learning Methods
DockOpt: A Tool for Automatic Optimization of Docking Models
Graph Theoretical Means for Calculating Kekule and Hueckel Parameters in Benzenoid and Related Systems
Development and Validation of AMANDA, a New Algorithm for Selecting Highly Relevant Regions in Molecular Interaction Fields
New Hybrid Genetic Based Support Vector Regression as QSAR Approach for Analyzing Flavonoids-GABA(A) Complexes
Discovery of Novel Cathepsin S Inhibitors by Pharmacophore-Based Virtual High-Throughput Screening
A Robust and Efficient DNA Storage Architecture Based on Modulation Encoding and Decoding
Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator
Searching for Chemical Information in the Patent and Trademark Office
Computer systems for laboratory networks and high-performance NMR
Novel ZE-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis
PrimaDORAC: A Free Web Interface for the Assignment of Partial Charges, Chemical Topology, and Bonded Parameters in Organic or Drug Molecules
Correlation between the Metal and Organic Components, Structure Property, and Gas-Adsorption Capacity of Metal-Organic Frameworks
Molecular Mechanism of Biased Ligand Conformational Changes in CC Chemokine Receptor 7
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space
Book Review of Molecules and Medicine
RMG Database for Chemical Property Prediction
Cocry-pred: A Dynamic Resource Propagation Method for Cocrystal Prediction
Molecular Modeling of Neurokinin B and Tachykinin NK 3 Receptor Complex
Graph with Residue-Based Cross-Modal Framework Enhances Cell Function-Related Protein Properties Prediction
Graph-Based Machine Learning Framework for Predicting Hydrogen Storage Capacity in Metal-Organic Frameworks
Three-Dimensional Molecular Descriptors Based on Electron Charge Density Weighted Graphs
Open-Source Machine Learning in Computational Chemistry
Blind Pose Prediction, Scoring, and Affinity Ranking of the CSAR 2014 Dataset
Role of Residues Undergoing Hereditary Spastic Paraplegias Mutations: Insights from Simulating the Spiral to Ring Transition in Katanin
Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites
A New Approach to Design Virtual Combinatorial Library with Genetic Algorithm Based on 3D Grid Property
Novel Atomic-Level-Based AI Topological Descriptors: Application to QSPR/QSAR Modeling
Virtual Screening of Abl Inhibitors from Large Compound Libraries by Support Vector Machines
Similarity Approach to Chemical Reactivity. Overlap Determinant Method in the Chemistry of Complex Reactions with Coarctate Transition States
Molecular Docking of Carbohydrate Ligands to Antibodies: Structural Validation against Crystal Structures
Application of Nearest-Neighbor and Cluster Analyses in Pharmaceutical Lead Discovery
ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs
From Chemical Topology to Three-Dimensional Geometry. Edited by Alexandru T. Balaban. Plenum Press: New York, 1997, xvii + 420 pp. ISBN 0-306-45462-9
Comparative Exploration on Quantifying Molecular Diversity
From Knowledge Generation to Knowledge Archive. A General Strategy Using TOPS-MODE with DEREK To Formulate New Alerts for Skin Sensitization
Core Flipping in Lead Optimization: Rank Ordering Using λ-Dynamics
A Hyperbolic Discrete Diffusion 3D RNA Inverse Folding Model for Functional RNA Design
A Comprehensive Machine Learning Model for Metal-Ligand Binding Prediction: Applications in Chemistry and Biology
ProfhEX: Empowering Early Drug Discovery with Machine Learning-Based Target Profiling and Liability Prediction
Analysis of keywords in chemistry
Development of indexing and indexes
The Design of a Multipurpose File of Thermodynamic Data
Pseudonatural Products Occur Frequently in Biologically Relevant Compounds
Deciphering Protein Secondary Structures and Nucleic Acids in Cryo-EM Maps Using Deep Learning
Investigation of Melting Dynamics of Hafnium Clusters
Correction to "admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties"
Design and Test of Molecules that Interfere with the Recognition Mechanisms between the SARS-CoV-2 Spike Protein and Its Host Cell Receptors
Chemical Information Resources Directory: an integrating component of the Chemical Substances Information Network
Investigating Statistical Conditions of Coevolutionary Signals that Enable Algorithmic Predictions of Protein Partners
Assessing the Chemical Intelligence of Large Language Models
Mathematical Framework to Identify Optimal Molecule Based on Virtual Ligand Strategy
Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein
Problems in Physical Property Data Retrieval
DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields
Prior Knowledge for Predictive Modeling: The Case of Acute Aquatic Toxicity
Coarse-Grained Crystal Graph Neural Networks for Reticular Materials Design
A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS
Multidimensional Decomposition and Ensemble Modeling of Histatin 1 and Its Siblings: Detailing Structure and Biological Function Using an Integrative Approach
Diverse uses and future prospects for Wiswesser line-formula notation
Online searching of polymer patents: precision and recall
FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses
FLAME: A Program to Flexibly Align Molecules
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions
Chemical Information Instruction in Academe: Recent and Current Trends
Arylamide as Potential Selective Inhibitor for Matrix Metalloproteinase 9 (MMP9): Design, Synthesis, Biological Evaluation, and Molecular Modeling
Molecular Dynamics Simulations of PAMAM and PPI Dendrimers Using the GROMOS-Compatible 2016H66 Force Field
Conformational Analysis of Aliskiren, a Potent Renin Inhibitor, Using High-Resolution Nuclear Magnetic Resonance and Molecular Dynamics Simulations
Rescoring Virtual Screening Results with the MM-PBSA Methods: Beware of Internal Dielectric Constants
Enrichment of High-Throughput Screening Data with Increasing Levels of Noise Using Support Vector Machines, Recursive Partitioning, and Laplacian-Modified Naive Bayesian Classifiers
Topological approach of carbon-13 NMR spectral simulation: Application to fuzzy substructures
Applications of Artificial Intelligence for Chemical Inference. XVI. Computer Generation of Vertex-Graphs and Ring Systems
A new scheme for assignment of a canonical connection table
Learning Force Field Parameters from Differentiable Particle-Field Molecular Dynamics
Symmetry-Adapted Bases of Matrix Spaces Applied to Quantum Chemistry
Validation of Free Energy Methods in AMBER
Edifice
Computational Analysis of a Next-Generation Platinum-Based Chemotherapies that Induce DNA Double-Strand Breaks
Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework
Discovery and Evaluation of Anti-Fibrinolytic Plasmin Inhibitors Derived from 5-(4-Piperidyl)isoxazol-3-ol (4-PIOL)
Women Make COMP: Mentoring the Next Generation of Women in Computational Chemistry
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction
Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs
Retro Drug Design: From Target Properties to Molecular Structures
Similarity Searching for Potent Compounds Using Feature Selection
Automated Annotation of Sites of Metabolism from Biotransformation Data
Combinatorial Library Design: Maximizing Model-Fitting Compounds within Matrix Synthesis Constraints
Patent Information Activity of the Technical Information Retrieval Committee of the Manufacturing Chemists' Association
Partial Molecular Alignment via Local Structure Analysis
PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS
Discovery of Ubiquitin-Specific Protease 7 (USP7) Inhibitors with Novel Scaffold Structures by Virtual Screening, Molecular Dynamics Simulation, and Biological Evaluation
Topology-Aided Molecular Design: The Platonic Molecules of Genera 0 to 3
The Characterization of Chemical Structures Using Molecular Properties. A Survey
Use of Reduced Graphs To Encode Bioisosterism for Similarity-Based Virtual Screening
Mechanisms for Flavin-Mediated Oxidation: Hydride or Hydrogen-Atom Transfer?
PaCS-Q: Python Toolkits for Path Sampling in MD and QM/MM MD Simulation
Chemical Combinatorics for Alkane-Isomer Enumeration and More
CAML: Commutative Algebra Machine Learning─A Case Study on Protein-Ligand Binding Affinity Prediction
Applications of graph theory and topology for the study of aromaticity in inorganic compounds
Kohonen Network Study of Aromatic Compounds Based on Electronic and Nonelectronic Structure Descriptors
Prediction of the Intrinsic Hydrogen Bond Acceptor Strength of Organic Compounds by Local Molecular Parameters
Searches for polymers in the BASIC files derived from the Chemical Abstracts Service Chemical Registry System
A new approach to information retrieval problems in separations science
Matrix formalism of the mnemonic diagram for thermodynamic relationships
Insights into the Dynamics and Dissociation Mechanism of a Protein Redox Complex Using Molecular Dynamics
PaCh (Packed Chemicals): Computationally Effective Binary Format for Chemical Structure Encoding
On the Role of Entropy in the Stabilization of α-Helices
CoMFA 3D-QSAR Analysis of HIV-1 RT Nonnucleoside Inhibitors, TIBO Derivatives Based on Docking Conformation and Alignment
New Manuscript Type: Application Note
Development of Novel Statistical Potentials Describing Cation-pi Interactions in Proteins and Comparison with Semiempirical and Quantum Chemistry Approaches
Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers
Lingos, Finite State Machines, and Fast Similarity Searching
A Mechanistic Hypothesis for the Cytochrome P450-Catalyzed Cis-Trans Isomerization of 4-Hydroxytamoxifen: An Unusual Redox Reaction
Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach
Three Dissimilarity Measures to Contrast Dendrograms
Combination of Molecular Dynamics Simulations and Machine Learning Reveals Structural Characteristics of Stereochemistry-Specific Interdigitation of Synthetic Monomycoloyl Glycerol Analogs
Understanding Conformation Importance in Data-Driven Property Prediction Models
Generative Models for Molecular Design
ZINC: A Free Tool to Discover Chemistry for Biology
Combining Unsupervised and Supervised Artificial Neural Networks to PredictAquatic Toxicity
Resolving Molecular Interactions in Protein Folding Trajectories with NCIPLOT
Structural Bias in Three-Dimensional Autoregressive Generative Machine Learning of Organic Molecules
Lessons in Molecular Recognition, 2. Assessing and Improving Cross-Docking Accuracy
A Simple Framework for Collaborative Development of Predictive Models Trained on Proprietary Data
Heuristic approach for displaying chemical structures
Correction to "SolTranNet - A Machine Learning Tool for Fast Aqueous Solubility Prediction"
Preparing Scientific Illustrations: A Guide to Better Posters, Presentations, and Publications, 2nd ed. By Mary Helen Briscoe, Springer: New York, 1996, 204 pp, ISBN 0-387-94581-4
A Factorial Design To Optimize Cell-Based Drug Discovery Analysis
The Development and Application of KinomePro-DL: A Deep Learning Based Online Small Molecule Kinome Selectivity Profiling Prediction Platform
Novel Scoring Functions Comprising QXP, SASA, and Protein Side-Chain Entropy Terms
Molecular Insights into 14-Membered Macrolides Using the MM-PBSA Method
Efficient Application of 2D NMR Correlation Information in Computer-Assisted Structure Elucidation of Complex Natural Products
Large-Scale Docking in the Cloud
Unsupervised 3D Ring Template Searching as an Ideas Generator for Scaffold Hopping: Use of the LAMDA, RigFit, and Field-Based Similarity Search (FBSS) Methods
Assessment of Experimental Bond Dissociation Energies Using Composite ab Initio Methods and Evaluation of the Performances of Density Functional Methods in the Calculation of Bond Dissociation Energies
Predictive Carcinogenicity: A Model for Aromatic Compounds, with Nitrogen-Containing Substituents, Based on Molecular Descriptors Using an Artificial Neural Network
Automated Analysis of Soft Matter Interfaces, Interactions, and Self-Assembly with PySoftK
Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal
A momentum-space approach to molecular similarity
New Developments in Hydrogen Bonding Acidity and Basicity of Small Organic Molecules for the Prediction of Physical and ADMET Properties. Part 2. The Universal Solvation Equation
On the Relation between the P'/P Index and the Wiener Number
Correction to "Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set"
Radical Scavenging Activity of Natural-Based Cassaine Diterpenoid Amides and Amines
Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces
Regression Modelability Index: A New Index for Prediction of the Modelability of Data Sets in the Development of QSAR Regression Models
What Is Aromaticity?
Choosing Feature Selection and Learning Algorithms in QSAR
MECHGEN: Computer Aided Generation and Reduction of Reaction Mechanisms
A Group-Theoretical Bound for the Number of Main Eigenvalues of a Graph
Predicting Energetics Materials' Crystalline Density from Chemical Structure by Machine Learning
DETHERM: Thermophysical property data for the optimization of heat-transfer equipment
CelS-Catalyzed Processive Cellulose Degradation and Cellobiose Extraction for the Production of Bioethanol
Constructing Interconsistent, Reasonable, and Predictive Models for Both the Kinetic and Thermodynamic Properties of HIV-1 Protease Inhibitors
Retrieval of Japanese scientific and technical information from the JICST online information system