yusuke1997/dblp-id-title huggingface dataset:
Optimized Protein-Excipient Interactions in the Martini 3 Force Field
Structure-Based Virtual Screening and Biological Evaluation of a Calpain Inhibitor for Prevention of Selenite-Induced Cataractogenesis in an in Vitro System
Modeling of the Water Network at Protein-RNA Interfaces
ASEDock-Docking Based on Alpha Spheres and Excluded Volumes
Correction to "Benchmarking Zinc-Binding Site Predictors: A Comparative Analysis of Structure-Based Approaches"
The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems
Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom
DeepIce: A Deep Neural Network Approach To Identify Ice and Water Molecules
Statistical analysis of atom topological neighborhoods and multivariate representations of a large chemical file
Accurate Prediction of ωB97X-D/6-31G* Equilibrium Geometries from a Neural Net Starting from Merck Molecular Force Field (MMFF) Molecular Mechanics Geometries
Dissecting the Role of the Hydroxyl Moiety at C14 in (+)-Opioid-Based TLR4 Antagonists via Wet-Lab Experiments and Molecular Dynamics Simulations
Visual Explanations. Images and Quantities, Evidence and Narrative By Edward R. Tufte. Graphics Press: Cheshire, Connecticut, 1997, 156 pp, ISBN 0-9613921-2-6
Calculation of electrostatic potential maps and atomic charges for large molecules
Fundamental Principles of Molecular Modeling. Edited by W. Gans, A. Amann, and J. C. A. Boeyens. Plenum Press: New York, 1996, 249 pp. ISBN 0-306-45305-3
Opportunities for alternative suppliers of secondary chemical information
2-Difluoromethylthio-4, 6-bis(monoalkylamino)-1, 3, 5-triazines as Inhibitors of Hill Reaction: A QSAR Study with Orthogonalized Descriptors
High-Throughput Optimization of a High-Pressure Catalytic Reaction
Neural Networks in QSAR and Drug Design. Edited by J. Devillers. Volume 2 in the Series: Principles of QSAR and Drug Design. Academic Press: San Diego, 1996, 284 pp. ISBN 0-12-213815-5
A Multiscale Simulation System for the Prediction of Drug-Induced Cardiotoxicity
High-Throughput Prediction of Metal-Embedded Complex Properties with a New GNN-Based Metal Attention Framework
Monte Carlo Simulations of Free and Confined Walks in Reflecting Statistics
MMSyn: A New Multimodal Deep Learning Framework for Enhanced Prediction of Synergistic Drug Combinations
Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution
Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method
Sharing Data from Molecular Simulations
Machine Learning in Drug Discovery
Partitioning of pi-Electrons in Rings of Polycyclic Conjugated Hydrocarbons. 5. Nonalternant Compounds
DeepMFFGO: A Protein Function Prediction Method for Large-Scale Multifeature Fusion
The Blue Obelisk-Interoperability in Chemical Informatics
Probabilistic Isolation of Crystalline Inorganic Phases
Classical and Three-Dimensional QSAR in Agro-chemistry. Edited by Corwin Hansch and Toshio Fujita. ACS Symposium Series 606. American Chemical Society: Washington, 1995, x + 342 pp, ISBN 0-8412-3321-7
Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles
SCUBIDOO: A Large yet Screenable and Easily Searchable Database of Computationally Created Chemical Compounds Optimized toward High Likelihood of Synthetic Tractability
Multimode Ligand Binding in Receptor Site Modeling: Implementation in CoMFA
Accelerated Design for High-Entropy Alloys Based on Machine Learning and Multiobjective Optimization
NBS Standard Reference Database, NBS/EPA/MSDC Mass Spectral Database PC version
Integrated Project Views: Decision Support Platform for Drug Discovery Project Teams
SteamTab: Thermodynamic and Transport Properties of Steam
Mold 2 , Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics
Topological Organic Chemistry. 12. Whole-Molecule Schultz Topological Indices of Alkanes
Prediction of Henry's Law Constants of Triazine Derived Herbicides from Quantum Chemical Continuum Solvation Models
Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks
Topological Approach to Analgesia
A new system for the designation of chemical compounds. 2. Coding of cyclic compounds
Selective Fusion of Heterogeneous Classifiers for Predicting Substrates of Membrane Transporters
Structure-Preserving Joint Non-negative Tensor Factorization to Identify Reaction Pathways Using Bayesian Networks
Delving into Macrolide Binding Affinities and Associated Structural Modulations in Erythromycin Esterase C: Insights into the Venus Flytrap Mechanism
Data and Molecular Fingerprint-Driven Machine Learning Approaches to Halogen Bonding
Quantitative Structure-Activity Relationship Modeling of Juvenile Hormone Mimetic Compounds for Culex P ipiens Larvae, with a Discussion of Descriptor-Thinning Methods
Ensemble of Linear Models for Predicting Drug Properties
Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles
Atom Equivalent Energies for the Rapid Estimation of the Heat of Formation of Explosive Molecules from Density Functional Tight Binding Theory
Differential Multimolecule Fingerprint for Similarity Search─Making Use of Active and Inactive Compound Sets in Virtual Screening
SIRAH Tools GUI: An Intuitive Interface for the Analysis of CG Simulations
Novel Characterization of Proteomics Maps by Sequential Neighborhoods of Protein Spots
FATE, the environmental fate constants information database
Large-Scale Analysis of Bioactive Ligand Conformational Strain Energy by Ab Initio Calculation
Classification Mapping and Its Application on Chemical Systems
Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers
Structure-Activity Relationship Studies of Substituted 17-Acetoxyprogesterone Hormones
Network-Driven Methods Using Gene Expression Signatures to Find Therapeutic Targets in Breast Cancer Validated via Molecular Dynamics Studies
DeepExpDR: Drug Response Prediction through Molecular Topological Grouping and Substructure-Aware Expert
Neural Network-Based Filter Design for Compressive Raman Classification of Cells
Multiscale Computational Protocols for Accurate Residue Interactions at the Flexible Insulin-Receptor Interface
Locating Multiple Transition Pathways for Complex Biomolecules
Structural Insights into 5-HT 1A /D 4 Selectivity of WAY-100635 Analogues: Molecular Modeling, Synthesis, and in Vitro Binding
DeepChemStable: Chemical Stability Prediction with an Attention-Based Graph Convolution Network
Chemical Language Model Linker: Blending Text and Molecules with Modular Adapters
Solving the 3-SAT Problem Based on DNA Computing
Steric Trigger as a Mechanism for CB 1 Cannabinoid Receptor Activation
Combining Physics-Based Protein-DNA Energetics with Machine Learning to Predict Interpretable Transcription Factor-DNA Binding
ChemDataExtractor 2.0: Autopopulated Ontologies for Materials Science
Applications of the Wiswesser line notation at the Dow Chemical Company
Template CoMFA: The 3D-QSAR Grail?
Structure-reaction type paradigm in the conventional methods of describing organic reactions and the concept of imaginary transition structures overcoming this paradigm
PLS-Optimal: A Stepwise D-Optimal Design Based on Latent Variables
Prioritizing Virtual Screening with Interpretable Interaction Fingerprints
Dynamic Training Enhances Machine Learning Potentials for Long-Lasting Molecular Dynamics
ChatGPT Generated Content and Similarity Index in Chemistry
Structure Based Model for the Prediction of Phospholipidosis Induction Potential of Small Molecules
Small Single-Stranded DNA Structure Prediction
Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators
lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures
Heuristic Extraction of Rules in Pruned Artificial Neural Networks Models Used for Quantifying Highly Overlapping Chromatographic Peaks
Graph Theoretical Invariant of Randic Revisited
SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening
A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit)
Machine Learning for Time-Resolved Selectivity Analysis in Methanol-To-Olefins Reaction
NMR simulator and IR simulator
Benzenoid series having a constant number of isomers. 2. Topological characteristics of strictly pericondensed constant-isomer benzenoid series
Broad Coverage of Commercially Available Lead-like Screening Space with Fewer than 350, 000 Compounds
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography
Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction
pmx Webserver: A User Friendly Interface for Alchemistry
Recognition and Binding of RsmE to an AGGAC Motif of RsmZ: Insights from Molecular Dynamics Simulations
HOMA Index Establishes Similarity to a Reference Molecule
MD-Based Assessment of Covalent Inhibitors in Noncovalent Association Complexes: Learning from Cathepsin K as a Test Case
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series
A Deep Retrieval-Enhanced Meta-Learning Framework for Enzyme Optimum pH Prediction
Scaffold Hopping Using Clique Detection Applied to Reduced Graphs
GGNpTCR: A Generative Graph Structure Neural Network for Predicting Immunogenic Peptides for T-cell Immune Response
Neural Network for Principle of Least Action
Interaction Patterns of Pyrazolopyrimidines with Receptor Proteins
Prediction of Nonlinear Optical Responses of Organic Compounds
VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening
FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption
Many-Body Optimization Using an Ab Initio Monte Carlo Method
A Web Service Infrastructure for Thermochemical Data
Orismology (the Science of Defining Words) and the Geometrical Foundations of Chemistry, 4. Polycyclic Compounds
Development of Quantitative Structure-Property Relationship Models for Early ADME Evaluation in Drug Discovery. 1. Aqueous Solubility
How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials
Experimental and Computational Study of Aryl-thiosemicarbazones Inhibiting Cruzain Reveals Reversible Inhibition and a Stepwise Mechanism
Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of Phthalates
Substrate Sequences Tell Similar Stories as Binding Cavities: Commentary
QSAR Modeling Based on Conformation Ensembles Using a Multi-Instance Learning Approach
Spec2D: A Structure Elucidation System Based on 1 H NMR and H-H COSY Spectra in Organic Chemistry
Assessment of the Macrocyclic Effect for the Complexation of Crown-Ethers with Alkali Cations Using the Substructural Molecular Fragments Method
Natural Language Processing Methods for the Study of Protein-Ligand Interactions
Aqueous Solubility Prediction of Drugs Based on Molecular Topology and Neural Network Modeling
Studies in deciphering the information content of chemical formulas: a comprehensive study of fluorenes and fluoranthenes
Structure-Based Virtual Screening Approach for Discovery of Covalently Bound Ligands
The Chemical Abstracts Service Chemical Registry System. VIII. Manual Registration
Determination of a Focused Mini Kinase Panel for Early Identification of Selective Kinase Inhibitors
Conjugated Quantitative Structure-Property Relationship Models: Application to Simultaneous Prediction of Tautomeric Equilibrium Constants and Acidity of Molecules
ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations
Predicting Binding Energies and Electronic Properties of Boron Nitride Fullerenes Using a Graph Convolutional Network
Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families
Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input
Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review
Machine Learning Enhanced Spectrum Recognition Based on Computer Vision (SRCV) for Intelligent NMR Data Extraction
HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes
Accelerating De Novo Drug Design against Novel Proteins Using Deep Learning
Prediction of Energetic Material Properties from Electronic Structure Using 3D Convolutional Neural Networks
eCounterscreening: Using QSAR Predictions to Prioritize Testing for Off-Target Activities and Setting the Balance between Benefit and Risk
Large-Scale Learning of Structure-Activity Relationships Using a Linear Support Vector Machine and Problem-Specific Metrics
Editorial - A Look at Philosophers Looking at Technology
Efficient Computation of Structural and Electronic Properties of Halide Perovskites Using Density Functional Tight Binding: GFN1-xTB Method
Molecular Structure Disassembly Program (MOSDAP): A Chemical Information Model To Automate Structure-Based Physical Property Estimation
Terse Literatures. III. The ARTEC Computer Program
SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules
KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination
A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning
Human Rhinovirus 3C Protease: Generation of Pharmacophore Models for Peptidic and Nonpeptidic Inhibitors and Their Application in Virtual Screening
Developing Descriptors To Predict Mechanical Properties of Nanotubes
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery
DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1
Chemical graph-theoretical cluster expansion and diamagnetic susceptibility
Fragment Database FDB-17
PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent
New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases
Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants"
Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase
Inferring Extended Virtual Knowledge from an EPIOS Conversion Graph of Overlapping Substructures
Experimental Algorithmic Generation of Articulated Index Entries from Natural Language Phrases at Chemical Abstracts Service
Rational Screening Set Design and Compound Selection: Cascaded Clustering
Identification and Visualization of Kinase-Specific Subpockets
Experience in developing an in-house molecular information and modeling system
A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations
Partitioning of pi-Electrons in Rings for Clar Structures of Benzenoid Hydrocarbons
Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning
The Large Data Base File Structure Dilemma
Write Like a Chemist
Matching Cavities in G Protein-Coupled Receptors to Infer Ligand-Binding Sites
Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques
Batched Bayesian Optimization for Drug Design in Noisy Environments
In Silico Design and Synthesis of Antifungal Peptides Guided by Quantitative Antifungal Activity
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
Machine Learning Guided Atom Mapping of Metabolic Reactions
Gaussian Process Regression-Based Near-Infrared d-Luciferin Analogue Design Using Mutation-Controlled Graph-Based Genetic Algorithm
Correction to Analyzing Learned Molecular Representations for Property Prediction
Nomenclature of macrocyclic compounds by sequential citation
Bayesian Flow Network Framework for Chemistry Tasks
On-Line Searching of the American Petroleum Institute's Databases
OntoKin: An Ontology for Chemical Kinetic Reaction Mechanisms
Reliability of Nonparametric Linear Classifers
Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies
A Computational Study of Intramolecular Proton Transfer in Gaseous Protonated Glycine
Scaffold-Hopped Compound Identification by Ligand-Based Approaches with a Prospective Affinity Test
Employing Automated Machine Learning (AutoML) Methods to Facilitate the In Silico ADMET Properties Prediction
Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex
Versatile Lipases from the Candida rugosa-like Family: A Mechanistic Insight Using Computational Approaches
Theoretical Prediction of Partition Coefficients via Molecular Electrostatic and Electronic Properties
A Fast Algorithm for Searching for Molecules Containing a Pharmacophore in Very Large Virtual Combinatorial Libraries
Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence
Neural Network Based Temperature-Dependent Quantitative Structure Property Relations (QSPRs) for Predicting Vapor Pressure of Hydrocarbons
A New Protocol for Predicting Novel GSK-3β ATP Competitive Inhibitors
Modeling Zinc Complexes Using Neural Networks
Eigen Value Analysis of HIV-1 Integrase Inhibitors
Analysis of the Calculated Physicochemical Properties of Respiratory Drugs: Can We Design for Inhaled Drugs Yet?
QSAR Study of 1, 8-Naphthyridin-4-ones As Inhibitors of Photosystem II
Modeling Heterogeneous Catalysis Using Quantum Computers: An Academic and Industry Perspective
Comparison of an Empirical and a Theoretical Linear Solvation Energy Relationship Applied to the Characterization of Solute Distribution in a Poly(ethylene) Glycol-Salt Aqueous Biphasic System
Model Carbyne Knots vs Ideal Knots
Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set
Ties in Proximity and Clustering Compounds
OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery
iRaPCA and SOMoC: Development and Validation of Web Applications for New Approaches for the Clustering of Small Molecules
Characterization of Protein-Ligand Chalcogen Bonds: Insights from Database Survey and Quantum Mechanics Calculations
Generative Models Should at Least Be Able to Design Molecules That Dock Well: A New Benchmark
Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials
Influence of the Conditions in Pharmacophore Generation, Scoring, and 3D Database Search for Chemical Feature-Based Pharmacophore Models: One Application Study of ET A - and ET B -Selective Antagonists
Flexsim-X: A Method for the Detection of Molecules with Similar Biological Activity
Searching for Substructures in Fragment Spaces
Computational Rationale for the Selective Inhibition of the Herpes Simplex Virus Type 1 Uracil-DNA Glycosylase Enzyme
The Sheffield Generic Structures Project-a Retrospective Review
ProCeSa: Contrast-Enhanced Structure-Aware Network for Thermostability Prediction with Protein Language Models
Primary journals today and tomorrow
The Variable Connectivity Index 1f versus the Traditional Molecular Descriptors: A Comparative Study of 1f Against Descriptors of CODESSA
Interactive Pattern Recognition in the Chemical Analysis Laboratory
Advances and Challenges in Computational Target Prediction
Polarizable Force Field of Intrinsically Disordered Proteins with CMAP and Reweighting Optimization
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes
Theoretical Derivation of Heuristic Molecular Lipophilicity Potential: A Quantum Chemical Description for Molecular Solvation
Graphics challenge WLN. Can WLN hold fast?
Starting material oriented retrosynthetic analysis in the LHASA program. 1. General description
Gene Expression Data Based Deep Learning Model for Accurate Prediction of Drug-Induced Liver Injury in Advance
Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery
Geometric Accuracy of Three-Dimensional Molecular Overlays
A ring-based chemical structural query system: use of a novel ring-complexity heuristic
Visualization and Interpretation of High Content Screening Data
Effect of the Generation of PAMAM Dendrimers on the Stabilization of Gold Nanoparticles
Identification of Novel Phosphodiesterase-4D Inhibitors Prescreened by Molecular Dynamics-Augmented Modeling and Validated by Bioassay
Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations
A Flexible Interactive Graphics System for Searching Atom Connectivity Matrices
Multi-Objective Genetic Algorithm (MOGA) As a Feature Selecting Strategy in the Development of Ionic Liquids' Quantitative Toxicity-Toxicity Relationship Models
Improved GNNs for Log D 7.4 Prediction by Transferring Knowledge from Low-Fidelity Data
Electrotopological State Indices for Atom Types: A Novel Combination of Electronic, Topological, and Valence State Information
RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks
Supervised Consensus Scoring for Docking and Virtual Screening
Machine-Learning-Based Cyclic Voltammetry Behavior Model for Supercapacitance of Co-Doped Ceria/rGO Nanocomposite
Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease
Some Notes on Randic-Razinger's Approach to Characterization of Molecular Shapes
Molecular Dynamics Simulation-Driven Focused Virtual Screening and Experimental Validation of Inhibitors for MTDH-SND1 Protein-Protein Interaction
ZINC20 - A Free Ultralarge-Scale Chemical Database for Ligand Discovery
In Silico Evaluation of Oligomeric Representations for Molecularly Imprinted Polymer Modeling Using a Biological Template
Screening of Matrix Metalloproteinases Available from the Protein Data Bank: Insights into Biological Functions, Domain Organization, and Zinc Binding Groups
Complementing the proof of the limit of relative atomic moments
Prediction of Biological Activity for High-Throughput Screening Using Binary Kernel Discrimination
Use of flexible queries for searching conformationally flexible molecules in databases of three-dimensional structures
Chemometrics: Views and Propositions
Violently Twisted and Strained Organic Molecules: A Descriptor System for Simple Coronoid Aromatics with a Moebius Half-Twist and Semiempirical Calculations on the Moebius Analogs of Coronene
Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge
Exploring Protein Stability by Comparative Molecular Dynamics Simulations of Homologous Hyperthermophilic, Mesophilic, and Psychrophilic Proteins
PZIM: A Method for Similarity Searching Using Atom Environments and 2D Alignment
Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout
Improving the Quantification of Highly Overlapping Chromatographic Peaks by Using Product Unit Neural Networks Modeled by an Evolutionary Algorithm
Introducing and Implementing On-Line Bibliographic Retrieval Services in a Scientific Research and Development Organization
Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics
SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization