yusuke1997/dblp-id-title huggingface dataset:
Virtual Screen for Ligands of Orphan G Protein-Coupled Receptors
Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation
Description of organic reactions based on imaginary transition structures. 8. Synthesis space attached by a charge space and three-dimensional imaginary transition structures with charges
Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures
Machine Learning Predicts Degree of Aromaticity from Structural Fingerprints
Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening
Understanding the Excited-State Relaxation Mechanisms of Xanthophyll Lutein by Multi-configurational Electronic Structure Calculations
Parallel Algorithms for Graph Cycle Extraction Using the Cyclical Conjunction Operator
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning
QSAR and QSPR Studies of a Highly Structured Physicochemical Domain
RosettaAMRLD: A Reaction-Driven Approach for Structure-Based Drug Design from Combinatorial Libraries with Monte Carlo Metropolis Algorithms
Unraveling the Modulation of the Activity in Drugs Based on Methylated Phenanthroline When Intercalating between DNA Base Pairs
Noise-Consistent Hypergraph Autoencoder Based on Contrastive Learning for Cancer ceRNA Association Prediction in Complex Biological Regulatory Networks
Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched?
Calculations of the Free Energy of Interaction of the c-Fos-c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site
A Unique Chemical Fragmentation System for Indexing Patent Literature
Performance Assessment of Semiempirical Molecular Orbital Methods in Describing Halogen Bonding: Quantum Mechanical and Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Study
A Probabilistic Approach in the Search Space of the Molecular Distance Geometry Problem
Computational Lipidomics Reveals Environment-Specific Membrane Remodeling in Prostate Cancer
Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases
On-Line Substructure Searching Utilizing Wiswesser Line Notations
Studies of Ligand Diffusion Pathways over a Protein Surface
QSAR with Few Compounds and Many Features
Health and Safety Information for Regulatory Pruposes-An Industrial Point of View
Improving Predictions of Molecular Properties with Graph Featurization and Heterogeneous Ensemble Models
Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method
Development of QSAR Models To Predict and Interpret the Biological Activity of Artemisinin Analogues
DiSCuS: An Open Platform for (Not Only) Virtual Screening Results Management
Accurate Atom-Mapping Computation for Biochemical Reactions
Modeling Blood-Brain Barrier Partitioning Using the Electrotopological State
Theoretical Studies on the Interactions and Interferences of HIV-1 Glycoprotein gp120 and Its Coreceptor CCR5
E min : A First-Principles Thermochemical Descriptor for Predicting Molecular Synthesizability
A computerized metabolic map
Development and Application of a Data-Driven Reaction Classification Model: Comparison of an Electronic Lab Notebook and Medicinal Chemistry Literature
Enhancing the Effectiveness of Virtual Screening by Fusing Nearest Neighbor Lists: A Comparison of Similarity Coefficients
Acceleration of Graph Neural Network-Based Prediction Models in Chemistry via Co-Design Optimization on Intelligence Processing Units
Evaluating Machine Learning Models for Molecular Property Prediction: Performance and Robustness on Out-of-Distribution Data
Rule-Based Prediction Models of Cytochrome P450 Inhibition
Development of a Spectral Clustering Method for the Analysis of Molecular Data Sets
Small Molecular Oligopeptides Adorned with Tryptophan Residues as Potent Antitumor Agents: Design, Synthesis, Bioactivity Assay, Computational Prediction, and Experimental Validation
Subtle Structural Changes in Tetrahydroquinolines, A New Class of Nonsteroidal Selective Androgen Receptor Modulators, Induce Different Functions
Elucidation of Allosteric Inhibition Mechanism of 2-Cys Human Peroxiredoxin by Molecular Modeling
Analysis of Neighborhood Behavior in Lead Optimization and Array Design
Chemical Markup, XML, and the World Wide Web. 4. CML Schema
Estimation of the Aqueous Solubility of Organic Molecules by the Group Contribution Approach
Prediction of Cytochrome P450 3A4, 2D6, and 2C9 Inhibitors and Substrates by Using Support Vector Machines
Introduction to symposium on the development and use of reliable data bases for quantitative structure-activity relationships
QSARtuna: An Automated QSAR Modeling Platform for Molecular Property Prediction in Drug Design
A Kinetic Approach to the Random f-Graph Process with Nonuniform Edge Probabilities
Exploring Drug Repurposing for Influenza A (H3N2) Virus: A Computational Approach to Identifying Commercialized Drugs Targeting Hemagglutinin, Neuraminidase, and Nucleoprotein
An improved IUPAC-based method for identifying alkanes
Thermophysical Properties of the Lennard-Jones Fluid: Database and Data Assessment
Periodic Cages
Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking
AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models
Using Surrogate Modeling in the Prediction of Fibrinogen Adsorption onto Polymer Surfaces
Proton and carbon-13 NMR spectra simulation
Characterizing the Cooperative Effect of PROTAC Systems with End-Point Binding Free Energy Calculation
Discovery of Novel Acetylcholinesterase Inhibitors by Virtual Screening, In Vitro Screening, and Molecular Dynamics Simulations
Molecules in Wikipedia: Analysis of Their Chemical Diversity, Functional Roles, and Popularity
Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening
Perspectives on Knowledge Discovery Algorithms Recently Introduced in Chemoinformatics: Rough Set Theory, Association Rule Mining, Emerging Patterns, and Formal Concept Analysis
Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014
Report and Application of a Tool Compound Data Set
Hydrolysis Mechanism of the Linkers by Matrix Metalloproteinase-9 Using QM/MM Calculations
Computer Techniques for the Indexing of Chemical Reaction Information
Molecular Dynamics Simulations and Structural Analysis of Giardia duodenalis 14-3-3 Protein-Protein Interactions
Novel Shape Descriptors for Molecular Graphs
Molecular Basis for Impacts of DSIF on the Dynamics of RNA Polymerase II Elongation Complex
The substance module: the representation, storage, and searching of complex structures
Error Detection, Recovery, and Repair in the Translation of Inorganic Nomenclatures, 1. A Study of the Problem
Mapping Ligand-Shape Space for Protein-Ligand Systems: Distinguishing Key-in-Lock and Hand-in-Glove Proteins
3-Input AND Molecular Logic Gate with Enhanced Fluorescence Output: The Key Atom for the Accurate Prediction of the Spectra
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs
SCSA Code: Applications on the Cyclopeptide Renieramide
Using Molecular Quantum Similarity Measures under Stochastic Transformation To Describe Physical Properties of Molecular Systems
PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing
Deciphering Fine Molecular Details of Proteins' Structure and Function with a Protein Surface Topography (PST) Method
Distribution of Bound Conformations in Conformational Ensembles for X-ray Ligands Predicted by the ANI-2X Machine Learning Potential
Improved Solubility Predictions in scCO 2 Using Thermodynamics-Informed Machine Learning Models
The Role of Key Amino Acids in the Antimicrobial Mechanism of a Bacteriocin Model Revealed by Molecular Simulations
Estimation of Carcinogenicity Using Molecular Fragments Tree
Denoising Drug Discovery Data for Improved Absorption, Distribution, Metabolism, Excretion, and Toxicity Property Prediction
Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking
Extended Multitarget Pharmacology of Anticancer Drugs
Local Normal Mode Analysis for Fast Loop Conformational Sampling
Host-enhanced chemical indexing in technical databases
Structure-Based Kinase Profiling To Understand the Polypharmacological Behavior of Therapeutic Molecules
AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization
Uncovering the ATP-Dependent Activation Mechanism of NLRP3 through Integrated Computational Approaches
Data base development and search algorithms for automated infrared spectral identification
ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites
Effect of Halogen Substitutions on dUMP to Stability of Thymidylate Synthase/dUMP/mTHF Ternary Complex Using Molecular Dynamics Simulation
Performance Validation of Neural Network Based 13 C NMR Prediction Using a Publicly Available Data Source
The Relationship between the Sequence Identities of Alpha Helical Proteins in the PDB and the Molecular Similarities of Their Ligands
Alternative Algebraic Perspectives on CO/H 2 PROX over MnO 2 Composite Catalysts
Partitioning of pi-Electrons in Rings of Polycyclic Benzenoid Hydrocarbons. 2. Catacondensed Coronoids
Alkaline Phosphatases: in Silico Study on the Catalytic Effect of Conserved Active Site Residues Using Human Placental Alkaline Phosphatase (PLAP) As a Model Protein
Topological Organic Chemistry, 9. Graph Theory and Molecular Topological Indices of Stereoisomeric Organic Compounds
ReLMole: Molecular Representation Learning Based on Two-Level Graph Similarities
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods
Elucidating Antibiotic Permeation through the Escherichia coli Outer Membrane: Insights from Molecular Dynamics
Prediction of mass spectra from structural information
How Does the P7C3-Series of Neuroprotective Small Molecules Prevent Membrane Disruption?
Comparative Spectra Analysis (CoSA): Spectra as Three-Dimensional Molecular Descriptors for the Prediction of Biological Activities
Structure and Ligand-Based Design of mTOR and PI3-Kinase Inhibitors Leading to the Clinical Candidates VS-5584 (SB2343) and SB2602
Bridging Molecular Docking to Membrane Molecular Dynamics To Investigate GPCR-Ligand Recognition: The Human A 2A Adenosine Receptor as a Key Study
Employing Machine Learning Models to Predict Potential α-Glucosidase Inhibitory Plant Secondary Metabolites Targeting Type-2 Diabetes and Their In Vitro Validation
Quantitative Structure-Activity Relationship Models of Chemical Transformations from Matched Pairs Analyses
The Role of Charge Distribution on the Antimalarial Activity of Artemisinin Analogues
Incorporating Target-Specific Pharmacophoric Information into Deep Generative Models for Fragment Elaboration
Molecular Dynamics Simulations of Photo-Induced Free Radical Polymerization
Heuristic Search Algorithms for the Determination of Rate Constants and Reaction Mechanisms from Limited Concentration Data
Understanding and Predicting Ligand Efficacy in the μ-Opioid Receptor through Quantitative Dynamical Analysis of Complex Structures
Patent Intelligence and Technology-Gleaning Pseudoproprietary Information from Publicly Available Data
Biased Agonist TRV027 Determinants in AT1R by Molecular Dynamics Simulations
Structure-Based Rational Design of Novel Inhibitors Against Fructose-1,6-Bisphosphate Aldolase from Candida albicans
Augmenting Connectivity Information by Compound Name Parsing: Automatic Assignment of Stereochemistry and Isotope Labeling
On A Four-Dimensional Representation of DNA Primary Sequences
Correction to "Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus"
Automating Deep Learning-Based Generation and Evaluation of De Novo Chemical Reaction with ChemRxnSAGE
DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories
FFMDFPA: A FAIRification Framework for Materials Data with No-Code Flexible Semi-Structured Parser and Application Programming Interfaces
protPheMut: An Interpretable Machine Learning Tool for Classification of Cancer and Neurodevelopmental Disorders in Human Missense Mutations
H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site
Prediction of Infinite Dilution Activity Coefficients of Organic Compounds in Aqueous Solution from Molecular Structure
BP-Dock: A Flexible Docking Scheme for Exploring Protein-Ligand Interactions Based on Unbound Structures
R -NN Curves: An Intuitive Approach to Outlier Detection Using a Distance Based Method
A Practical Guide to Combinatorial Chemistry Edited by Anthony W. Czarnik and Sheila H. DeWitt. ACS Professional Reference Book. American Chemical Society: Washington, DC, 1997, 450 pp, ISBN 0-8412-3485-x
CovCysPredictor: Predicting Selective Covalently Modifiable Cysteines Using Protein Structure and Interpretable Machine Learning
Use of augmented Lagrangians in the calculation of molecular conformations by distance geometry
CMDmpnn: Combining Comparative Molecular Dynamics and ProteinMPNN to Rapidly Expand Enzyme Substrate Spectrum
TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials
Substituent Effect on the Photophysics and ESIPT Mechanism of N, N′-Bis(salicylidene)-p-phenylenediamine: A DFT/TD-DFT Analysis
Thompson Sampling─An Efficient Method for Searching Ultralarge Synthesis on Demand Databases
Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures
Identification of Phelligridin-Based Compounds as Novel Human CD73 Inhibitors
TEMPL: A Template-Based Protein-Ligand Pose Prediction Baseline
Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
Similarity Based Docking
Virtual Screening for Ligands of the Insect Molting Hormone Receptor
BitBIRCH Clustering Refinement Strategies
Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis
Storing Images in DNA via base128 Encoding
Chemical information science coverage in Chemical Abstracts
Two samples interleaved carbon hydrogen nitrogen microanalysis and its program design
Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors
APIPred: An XGBoost-Based Method for Predicting Aptamer-Protein Interactions
Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery
Curating and Visualizing the Analytical Methods and the Open Spectral Database's Chemical Functional Use Taxonomy
Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets
Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets
Enantiomeric Labeling of Reaction Graphs
Relativistic Pseudopotentional Incorporating Core/Valence Polarization and Nonlocal Effects
An Evaluation of the Leading Patent Equivalents Services
Statistically Validated QSARs, Based on Theoretical Descriptors, for Modeling Aquatic Toxicity of Organic Chemicals in Pimephales p romelas (Fathead Minnow)
Large-Scale Assessment of Activity Landscape Feature Probabilities of Bioactive Compounds
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes
Spectral Moments of the Edge Adjacency Matrix in Molecular Graphs. Benzenoid Hydrocarbons
Implementation of the Molecular Electrostatic Potential over Graphics Processing Units
Bioisosteric Similarity of Molecules Based on Structural Alignment and Observed Chemical Replacements in Drugs
Error Bounds on the SCISSORS Approximation Method
Scalable Partitioning and Exploration of Chemical Spaces Using Geometric Hashing
Sequence-Dependent Binding of Flavonoids to Duplex DNA
Unique, Unambiguous Representation of Chemical Structures by Computerization of a Simple Notation
PbImpute: Precise Zero Discrimination and Balanced Imputation in Single-Cell RNA Sequencing Data
QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena?
An International Mass Spectral Search System (MSSS). V. A Status Report
Comparison between the Vertex- and Edge-Connectivity Indices for Benzenoid Hydrocarbons
3D-Quantitative Structure-Activity Relationships of HEPT Derivatives as HIV-1 Reverse Transcriptase Inhibitors, Based on Ab Initio Calculations
An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes
PoreMatMod.jl: Julia Package for in Silico Postsynthetic Modification of Crystal Structure Models
JGromacs: A Java Package for Analyzing Protein Simulations
Retrospective Docking Study of PDE4B Ligands and an Analysis of the Behavior of Selected Scoring Functions
GEMS-Pack: A Graphical User Interface for the Packmol Program
Profile-QSAR 2.0: Kinase Virtual Screening Accuracy Comparable to Four-Concentration IC 50 s for Realistically Novel Compounds
Genetic Algorithm Managed Peptide Mutant Screening: Optimizing Peptide Ligands for Targeted Receptor Binding
Pairwise Difference Regression: A Machine Learning Meta-algorithm for Improved Prediction and Uncertainty Quantification in Chemical Search
Structure-activity relationships on pesticides: A development in methodology and its software system
Conserved Core Substructures in the Overlay of Protein-Ligand Complexes
Estimation of the Aqueous Solubility of Organic Molecules by the Group Contribution Approach, J. Chem. Inf. Comput. Sci. 41, 439-455 (2001)
Spatial Sign Preprocessing: A Simple Way To Impart Moderate Robustness to Multivariate Estimators
Differences in Gluco and Galacto Substrate-Binding Interactions in a Dual 6Pβ-Glucosidase/6Pβ-Galactosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis
NABhClassifier Server: A Tool for the Identification of Helical Nucleic Acid-Binding Sequences in Proteins
From Brazil to Germany: Challenges and Advantages
Graphical analysis and visualization of 3-D properties of molecules and solids
Ligand Binding Determinants for Angiotensin II Type 1 Receptor from Computer Simulations
GArNet: A Genetic Algorithm-Based Protein Redesign Approach to Optimize Mutation Combinations Informed by Network Theory
Prediction of Mutagenicity of Aromatic and Heteroaromatic Amines from Structure: A Hierarchical QSAR Approach
Global Bayesian Models for the Prioritization of Antitubercular Agents
Nomenclature and Coding of Fullerenes
Integrating Prior Chemical Knowledge into the Graph Transformer Network to Predict the Stability Constants of Chelating Agents and Metal Ions
Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure-Activity Relationship Studies
Erratum: 13 C NMR - Distance Matrix Descriptors: Optimal Abstract 3D Space Granularity for Predicting Estrogen Binding
Computer-aided molecular formula determination from mass, proton and carbon-13 NMR spectra
Scaffold Topologies. 2. Analysis of Chemical Databases
SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits
Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set
"SpectraGraph" and "SpectraSort": Mass spectral display and interpretation software for the Macintosh
Partially Unified Multiple Property Recursive Partitioning (PUMP-RP): A New Method for Predicting and Understanding Drug Selectivity
A Cellular Automata Model of an Aqueous Solution
Dual-Channel Multiscale Graph Transformer with Adversarial Contrastive Learning and Low-Rank Disentangled Stratified Negative Sampling for Drug Repositioning
scGANSL: Graph Attention Network with Subspace Learning for scRNA-seq Data Clustering
Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining
Gotcha GPT: Ensuring the Integrity in Academic Writing
Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction
Comparative Analysis of Polarizable and Nonpolarizable CHARMM Family Force Fields for Proteins with Flexible Loops and High Charge Density
Advancements in Nanobody Epitope Prediction: A Comparative Study of AlphaFold2Multimer vs AlphaFold3
Combining Stochastic Deformation/Relaxation and Intermolecular Contacts Analysis for Extracting Pharmacophores from Ligand-Receptor Complexes
Organic reaction database translation from REACCS to ORAC
The United Kingdom Chemical Database Service
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework
Conditional Probability: A New Fusion Method for Merging Disparate Virtual Screening Results
Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning
Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis
The Journal of Chemical Documentation and the Journal of Chemical Information and Computer Sciences : Publication and Citation Statistics
PATHFINDER II. A Computer Program That Generates Wiswesser Line Notations for Complex Polycyclic Structures
Guidelines for Recurrent Neural Network Transfer Learning-Based Molecular Generation of Focused Libraries
Assessing UFF and DFT-Tuned Force Fields for Predicting Experimental Isotherms of MOFs
Pharmacophore Modeling of Substituted 1, 2, 4-Trioxanes for Quantitative Prediction of their Antimalarial Activity
Prediction of Molecular Volume and Surface of Alkanes by Molecular Topology
Valid, Plausible, and Diverse Retrosynthesis Using Tied Two-Way Transformers with Latent Variables
De Novo Molecule Design Through the Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites
Study of E/Z Isomerization in a Series of Novel Non-ligand Binding Pocket Androgen Receptor Antagonists
Visual Characterization and Diversity Quantification of Chemical Libraries: 1. Creation of Delimited Reference Chemical Subspaces
Need for primary periodicals as determined by SDI
In Silico Prediction of Human Intravenous Pharmacokinetic Parameters with Improved Accuracy
Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition
Novel Chirality Descriptors Derived from Molecular Topology
Murine mPGES-1 3D Structure Elucidation and Inhibitors Binding Mode Predictions by Homology Modeling and Site-Directed Mutagenesis
2D Depiction of Protein-Ligand Complexes
Flux (1): A Virtual Synthesis Scheme for Fragment-Based de Novo Design
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials
Design and Diversity Analysis of Large Combinatorial Libraries Using Cell-Based Methods
PTM-Psi on the Cloud: A Cloud-Compatible Workflow for Scalable, High-Throughput Simulation of Post-Translational Modifications in Protein Complexes
Molecular Dynamics Simulations Reveal a Novel Mechanism for ATP Inhibition of Insulin Degrading Enzyme
Combining Horizontal and Vertical Substructure Relationships in Scaffold Hierarchies for Activity Prediction