yusuke1997/dblp-id-title huggingface dataset:
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations
Predicting Kinase Selectivity Profiles Using Free-Wilson QSAR Analysis
Setting the Record Straight: The Origin of the Pharmacophore Concept
Structural Characterization of Histatin 5-Spermidine Conjugates: A Combined Experimental and Theoretical Study
Neural Nets for the Simulation of Molecular Recognition within MS-Windows Environment
Sequential Superparamagnetic Clustering for Unbiased Classification of High-Dimensional Chemical Data
Mechanism of Ligand Discrimination by the NMT1 Riboswitch
A comparison of the MARPAT and Markush DARC software
Insights into the Catalytic Mechanism and Selectivity of S -Adenosyl Methionine (SAM)-Dependent Fluorinase toward Carbon-Halogen Bond Formation
Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery
Metadynamics as a Postprocessing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2
Interpreting Computational Neural Network QSAR Models: A Measure of Descriptor Importance
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators
Target-Independent Prediction of Drug Synergies Using Only Drug Lipophilicity
ESSESA: an expert system for elucidation of structures from spectra. 1. Knowledge base of infrared spectra and analysis and interpretation programs
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3
The Chemical Abstracts Service Chemical Registry System. VII. Tautomerism and Alternating Bonds
ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands
Photophysical Properties of S, Se and Te-Substituted Deoxyguanosines: Insight into Their Ability To Act as Chemotherapeutic Agents
Morgan revisited
Descriptor-First Approach for ADMET Prediction in the PolarisHub Antiviral Challenge
Random Walks and Chemical Graph Theory
Exploiting Cryo-EM Structural Information and All-Atom Simulations To Decrypt the Molecular Mechanism of Splicing Modulators
Discovery of Novel Pim-1 Kinase Inhibitors by a Hierarchical Multistage Virtual Screening Approach Based on SVM Model, Pharmacophore, and Molecular Docking
Public Domain HTS Fingerprints: Design and Evaluation of Compound Bioactivity Profiles from PubChem's Bioassay Repository
Experimental and Quantum Chemical Modeling Studies of the Interactions of l-Phenylalanine with Divalent Transition Metal Cations
Measuring Splitting and Overlapping in Molecular Systems. A Fuzzy Set Estimation of Reaction Hazards
End users and chemical information
Iterated Reaction Graphs: Simulating Complex Maillard Reaction Pathways
3DReact: Geometric Deep Learning for Chemical Reactions
The "Latent Membrane Permeability" Concept: QSPR Analysis of Inter/Intralaboratorically Variable Caco-2 Permeability
SANS Spectra with PLUMED: Implementation and Application to Metainference
Interpretation of Scoring Functions Using 3D Molecular Fields. Mapping the Diacyl-Hydrazine-Binding Pocket of an Insect Ecdysone Receptor
Combined Chemoinformatics Approach to Solvent Library Design Using clusterSim and Multidimensional Scaling
Generalized Spectral Moments of the Iterated Line Graphs Sequence. A Novel Approach to QSPR Studies
ChemStor: Using Formal Methods To Guarantee Safe Storage and Disposal of Chemicals
Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments
Molecular Similarity and Estimation of Molecular Properties
Predicting Antimalarial Activity in Natural Products Using Pretrained Bidirectional Encoder Representations from Transformers
Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning
Self-Consistent Component Increment Theory for Predicting Enthalpy of Formation
Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods
vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses
Charge Density in Enzyme Active Site as a Descriptor of Electrostatic Preorganization
Large-Scale Similarity Search Profiling of ChEMBL Compound Data Sets
Computer hardware and software in chemical information processing
Transferable Neural Network Potentials and Condensed Phase Properties
Catalytic Mechanism of Amyloid-β Peptide Degradation by Insulin Degrading Enzyme: Insights from Quantum Mechanics and Molecular Mechanics Style Møller-Plesset Second Order Perturbation Theory Calculation
CONAN─Novel Tool to Create and Analyze Liquids in Confined Space
Building a Kokumi Database and Machine Learning-Based Prediction: A Systematic Computational Study on Kokumi Analysis
Patch-Based Ray Tracing in NanoShaper Boosts Molecular Surface Computation
The Molecular Information File (MIF): Core Specifications of a New Standard Format for Chemical Data
Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA-Drug Associations
The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics
SAR Transfer across Different Targets
QSPR Using MOLGEN-QSPR: The Example of Haloalkane Boiling Points
Self-Configuring Radial Basis Function Neural Networks for Chemical Pattern Recognition
Virtual Target Screening: Validation Using Kinase Inhibitors
Computational Comparison of Imidazoline Association with the I2 Binding Site in Human Monoamine Oxidases
Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening
Capturing the Crystal: Prediction of Enthalpy of Sublimation, Crystal Lattice Energy, and Melting Points of Organic Compounds
Addressing Challenges of Identifying Geometrically Diverse Sets of Crystalline Porous Materials
Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond
CRISPro: An Automated Pipeline for Protein Conformation Stabilization by Proline
Allosteric Modulation Mechanism of the mGluR5 Transmembrane Domain
Diffusion Models in De Novo Drug Design
The NEIC Organic Analysis Reporting System
Highly Accurate and Explainable Predictions of Small-Molecule Antioxidants for Eight In Vitro Assays Simultaneously through an Alternating Multitask Learning Strategy
Database Searching for Compounds with Similar Biological Activity Using Short Binary Bit String Representations of Molecules
Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation
Recent Force Field Strategies for Intrinsically Disordered Proteins
Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations
Theoretical aspects of ring perception and development of the extended set of smallest rings concept
FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping
Computer perception of topological symmetry via canonical numbering of atoms
Matcher: An Open-Source Application for Translating Large Structure/Property Data Sets into Insights for Drug Design
From Linear to Nets: Multiconfiguration Polymer Structure Generation with PolyFlin
BiVAE-CPI: An Interpretable Generative Model Using a Bilateral Variational Autoencoder for Compound-Protein Interaction Prediction
Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A 2A Receptor
Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps
Training Based on Ligand Efficiency Improves Prediction of Bioactivities of Ligands and Drug Target Proteins in a Machine Learning Approach
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding
Neural networks and carbon-13 NMR shift prediction
COGNOS: A Beilstein-Type System for Organizing Organic Reactions
Pro-Search: Easy Online Information Retrieval for DIALOG
Computer-assisted synthetic analysis. A generalized procedure for subgoal transform selection based on a two-dimensional pattern language
Beneficent and Maleficent Effects of Cations on Bufadienolide Binding to Na+, K+-ATPase
DrugSK: A Stacked Ensemble Learning Framework for Predicting Drug Combinations of Multiple Diseases
Benchmarking Cross-Docking Strategies in Kinase Drug Discovery
Best Practices in Utilization of 2D-NMR Spectral Data as the Input for Chemometric Analysis in Biopharmaceutical Applications
MMDTA: A Multimodal Deep Model for Drug-Target Affinity with a Hybrid Fusion Strategy
Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results
Maximum Common Binding Modes (MCBM): Consensus Docking Scoring Using Multiple Ligand Information and Interaction Fingerprints
Structural Insights into Trapping and Dissociation of Small Molecules in K + Channels
Benchmark Performance of MultiCASE Inc. Software in Ames Mutagenicity Set
Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation
A Machine Learning-Based Modeling Approach for Dye Removal Using Modified Natural Adsorbents
Stacked Generalization with Applicability Domain Outperforms Simple QSAR on in Vitro Toxicological Data
Determining the Relative Binding Affinity of Ricin Toxin A Inhibitors by Using Molecular Docking and Nonequilibrium Work
Sequential Properties Representation Scheme for Recurrent Neural Network-Based Prediction of Therapeutic Peptides
An Algorithm for the Calculation of the Szeged Index of Benzenoid Hydrocarbons
Knowledge-Based Conformer Generation Using the Cambridge Structural Database
Deep Learning-Based Multimodal Fusion Approach for Predicting Acute Dermal Toxicity
Infrared Spectra Information and Their Correlation with QSAR Descriptors
Quadratic Shape Descriptors. 1. Rapid Superposition of Dissimilar Molecules Using Geometrically Invariant Surface Descriptors
Unleashing the Power of Knowledge Extraction from Scientific Literature in Catalysis
ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential
Conformalized Graph Learning for Molecular ADMET Property Prediction and Reliable Uncertainty Quantification
Excito-repellent and Pesticide-Likeness Properties of Essential Oils on Carpophilus dimidiatus (Fabricius) (Nitidulidae) and Oryzaephilus mercator (L.) (Silvanidae)
Understanding the Mechanism of Direct Activation of AMP-Kinase: Toward a Fine Allosteric Tuning of the Kinase Activity
HEPOM: Using Graph Neural Networks for the Accelerated Predictions of Hydrolysis Free Energies in Different pH Conditions
Computer-assisted synthetic analysis. Performance of tactical combinations of transforms
Effective Feature Selection Method for Class-Imbalance Datasets Applied to Chemical Toxicity Prediction
3DSEARCH: a system for three-dimensional substructure searching
An Uncertainty-Guided Deep Learning Method Facilitates Rapid Screening of CYP3A4 Inhibitors
Chemical information instruction of the undergraduate: a review and analysis
RNA-Specific Force Field Optimization with CMAP and Reweighting
k-Resonant Benzenoid Systems and k-Cycle Resonant Graphs
Atomdroid: A Computational Chemistry Tool for Mobile Platforms
Characterization of DNA Primary Sequences Based on the Average Distances between Bases
An Open Source Protein Gel Documentation System for Proteome Analyses
Correction to Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8
AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations
An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
Magic Rings: Navigation in the Ring Chemical Space Guided by the Bioactive Rings
Prediction of Water Distributions and Displacement at Protein-Ligand Interfaces
Integration of Structure-Activity Relationship and Artificial Intelligence Systems To Improve in Silico Prediction of Ames Test Mutagenicity
Elemental Benzenoids
Estimation of aqueous solubility of organic molecules by the group contribution approach. Application to the study of biodegradation
Computational Design of Myristoylated Cell-Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector-Binding Membrane Interface
Algebraic Chirality Criteria and Their Application to Chirality Classification in Rigid Molecular Systems
TRIOMPHE: Transcriptome-Based Inference and Generation of Molecules with Desired Phenotypes by Machine Learning
Computational Modeling of the Catalytic Mechanism of Human Placental Alkaline Phosphatase (PLAP)
The Management of a Large Data Base in IRIS
E a MEAD: Activation Energy Prediction of Cytochrome P450 Mediated Metabolism with Effective Atomic Descriptors
Method for Systematic Analogue Search Using the Mega SAR Matrix Database
Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides
Noble Gas Chemistry and the Fluoride Literature-What Influences Research Directions?
Problem-solving methods in computer-aided organic structure determination
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening
Chemical Genomics Approach for GPCR-Ligand Interaction Prediction and Extraction of Ligand Binding Determinants
Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations
Method for clustering proteins by use of all possible pairs of amino acids as structural descriptors
Comparative Molecular Field Analysis (CoMFA) of a Series of Symmetrical Bis-Benzamide Cyclic Urea Derivatives as HIV-1 Protease Inhibitors
The Centroid Approximation for Mixtures: Calculating Similarity and Deriving Structure-Activity Relationships
Computer-Assisted Learning Using a Dialogue System for Virtual Teacher-Student Communication
Building Quantitative Bridges between Dynamics and Sequences of SARS-CoV-2 Main Protease and a Diverse Set of Thirty-Two Proteins
Analysis of a Large Structure/Biological Activity Data Set Using Recursive Partitioning
Using Polynomial Smoothing and Data Bounding for the Detection of Adverse Process Changes in a Chemical Process
Pharmacophore Model for Wnt/Porcupine Inhibitors and Its Use in Drug Design
Unveiling Putative Excited State and Transmission of Binding Information in the Fluoride Riboswitch
ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data
Chemometrics: A Practical Guide By Kenneth R. Beebe, Randy J. Pell, and Mary Beth Seasholtz. Wiley-Interscience Series on Laboratory Automation. John Wiley & Sons: New York, 1998, xi + 348 pp, ISBN 0-471-12451-6
A Desktop Calculator for the Karplus Equation
De Novo Molecule Design Using Molecular Generative Models Constrained by Ligand-Protein Interactions
Bovine Serum Amine Oxidase and Polyamine Analogues: Chemical Synthesis and Biological Evaluation Integrated with Molecular Docking and 3-D QSAR Studies
The Impact of Supervised Learning Methods in Ultralarge High-Throughput Docking
Searching for Target-Selective Compounds Using Different Combinations of Multiclass Support Vector Machine Ranking Methods, Kernel Functions, and Fingerprint Descriptors
Relationships between Molecular Complexity, Biological Activity, and Structural Diversity
A Simple QSPR Model for Predicting Soil Sorption Coefficients of Polar and Nonpolar Organic Compounds from Molecular Formula
ChatGPT in the Material Design: Selected Case Studies to Assess the Potential of ChatGPT
Polarizable AMOEBA Model for Simulating Mg 2+ ·Protein·Nucleotide Complexes
Compositional Deep Probabilistic Models of DNA-Encoded Libraries
DOCKTITE - A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in the Molecular Operating Environment
NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering
BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank
Toward Understanding Mcl-1 Promiscuous and Specific Binding Mode
RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing
RetroGNN: Fast Estimation of Synthesizability for Virtual Screening and De Novo Design by Learning from Slow Retrosynthesis Software
3DSTarPred: A Web Server for Target Prediction of Bioactive Small Molecules Based on 3D Shape Similarity
Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2
Graph Theoretical Descriptors of Two-Dimensional Chirality with Possible Extension to Three-Dimensional Chirality
Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models
Amino Acid Sequence Autocorrelation Vectors and Ensembles of Bayesian-Regularized Genetic Neural Networks for Prediction of Conformational Stability of Human Lysozyme Mutants
The Mean Angular Distance Among Objects and Its Relationships with Kohonen Artificial Neural Networks
NeuroPred-AIMP: Multimodal Deep Learning for Neuropeptide Prediction via Protein Language Modeling and Temporal Convolutional Networks
CASPER: a computer program used for structural analysis of carbohydrates
Comparison of Combinatorial Clustering Methods on Pharmacological Data Sets Represented by Machine Learning-Selected Real Molecular Descriptors
Access to Polymer Information in Chemical Abstracts
IEV2Mol: Molecular Generative Model Considering Protein-Ligand Interaction Energy Vectors
Integrative Computational Approaches for TRPV1 Ion Channel Inhibitor Discovery: An Integrated Machine Learning, Drug Repurposing and Molecular Simulation Approach
Accurate Binding Free Energy Predictions in Fragment Optimization
An algorithm to identify and count coplanar isomeric molecules formed by the linear fusion of cyclopentane modules
Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies
Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating
Computational Method To Identify Druggable Binding Sites That Target Protein-Protein Interactions
Efficient Exploration of Chemical Compound Space Using Active Learning for Prediction of Thermodynamic Properties of Alkane Molecules
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field
Predictive Activity Profiling of Drugs by Topological-Fragment-Spectra-Based Support Vector Machines
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations
ReaxANA: Analysis of Reactive Dynamics Trajectories for Reaction Network Generation
GRAPH X
Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study
Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations
Automated de Novo Design of Olefin Metathesis Catalysts: Computational and Experimental Analysis of a Simple Thermodynamic Design Criterion
Nano-to-Microscale Mechanical Switches and Fuses Mediate Adhesive Contacts between Leukocytes and the Endothelium
Effective and Explainable Molecular Property Prediction by Chain-of-Thought Enabled Large Language Models and Multi-Modal Molecular Information Fusion
Understanding the Roles of the "Two QSARs"
Kernel-Based Partial Least Squares: Application to Fingerprint-Based QSAR with Model Visualization
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives
Identification of Selective, Cell Active Inhibitors of Protein Arginine Methyltransferase 5 through Structure-Based Virtual Screening and Biological Assays
Hydrophobicity─A Single Parameter for the Accurate Prediction of Disordered Regions in Proteins
Demystifying P2Y 1 Receptor Ligand Recognition through Docking and Molecular Dynamics Analyses
Effective Screening Strategy Using Ensembled Pharmacophore Models Combined with Cascade Docking: Application to p53-MDM2 Interaction Inhibitors
Mechanistic Insights into the Dioxygen Activation and Hydroxylation of Aliphatic C-H Bonds Catalyzed by the Heterobimetallic Manganese-Iron Hydroxylase AibH1H2 from Rhodococcus wratislaviensis
Description of organic reactions based on imaginary transition structures. 5. Recombination of reaction strings in a synthesis space and its application to the description of synthetic pathways
Interaction Nature and Computational Methods for Halogen Bonding: A Perspective
A Chinese Postman Problem Based on DNA Computing
Novel Scaffold Fingerprint (SFP): Applications in Scaffold Hopping and Scaffold-Based Selection of Diverse Compounds
CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions
Fast Protein Binding Site Comparison via an Index-Based Screening Technology
QSTR with Extended Topochemical Atom Indices. 2. Fish Toxicity of Substituted Benzenes
ACP-CLB: An Anticancer Peptide Prediction Model Based on Multichannel Discriminative Processing and Integration of Large Pretrained Protein Language Models
Notes on fully benzenoid hydrocarbons and their constant-isomer series
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides
Computer storage and retrieval of generic chemical structures in patents. 11. Theoretical aspects of the use of structure languages in a retrieval system
Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study
Discovery of Novel Inhibitors Targeting Human O-GlcNAcase: Docking-Based Virtual Screening, Biological Evaluation, Structural Modification, and Molecular Dynamics Simulation
Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit
Computer-assisted study of the relationship between molecular structure and surface tension of organic compounds
3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity
Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization
ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning
Simulation Reveals the Chameleonic Behavior of Macrocycles
dMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks
HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo
Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules
Prediction of Vapor Pressures of Hydrocarbons and Halohydrocarbons from Molecular Structure with a Computational Neural Network Model
Handling of Tautomerism and Stereochemistry in Compound Registration
Discovery of Novel Acetohydroxyacid Synthase Inhibitors as Active Agents against Mycobacterium tuberculosis by Virtual Screening and Bioassay
Molecular Dynamics Simulations of Polymer-Ionic Liquid (1-Ethyl-3-methylimidazolium Tetracyanoborate) Ternary Electrolyte for Sodium and Potassium Ion Batteries
Computation of Binding Energies Including Their Enthalpy and Entropy Components for Protein-Ligand Complexes Using Support Vector Machines
Fatty Acid and Retinol-Binding Protein: Unusual Protein Conformational and Cavity Changes Dictated by Ligand Fluctuations
Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator
Prediction of Chemical Biodegradability Using Support Vector Classifier Optimized with Differential Evolution
Mechanism of the Kolbe-Schmitt Reaction. Structure of the Intermediate Potassium Phenoxide-CO 2 Complex
Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide
CHEMiCALC. The Chemistry Companion
Rescaling of Point Charges as a Way to Improve the Simple-to-Use Electrostatic Embedding Scheme Developed to Explore Enzyme Activity with QM-Oriented Software
Inhibitor and Substrate Binding by Angiotensin-Converting Enzyme: Quantum Mechanical/Molecular Mechanical Molecular Dynamics Studies
Building Block-Centric Approach to DNA-Encoded Library Design
Elaborate Ligand-Based Modeling Reveals New Nanomolar Heat Shock Protein 90α Inhibitors