yusuke1997/dblp-id-title huggingface dataset:
Prediction of Chromatographic Retention Values (RM) and Partition Coefficients (log Poct) Using a Combination of Semiempirical Self-Consistent Reaction Field Calculations and Neural Networks
Reducing Docking Score Variations Arising from Input Differences
Conformational Analyses and MO Studies of f152A1 and Its Analogues as Potent Protein Kinase Inhibitors
Approaches to Understanding the Searching Behavior of CrossFire Users
New molecular modeling tools using three-dimensional chemical substructures
MOLGEN-CID - A Canonizer for Molecules and Graphs Accessible through the Internet
Spiral Coding of Leapfrog Polyhedra
Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model
Glycerol is Released from a New Path in MGL Lipase Catalytic Process
A Collective Property of Trees and Chemical Trees
Benchmarking of QSAR Models for Blood-Brain Barrier Permeation
Electronic and Steric Factors in the Stability of a Protofullerene Framework: Indacenoid Isomers of C30H12
Sophisticated algorithm for automatic extraction and analysis of substituent-induced chemical shift differences on carbon-13 NMR spectra
ElectroPredictor: An Application to Predict Mayr's Electrophilicity E through Implementation of an Ensemble Model Based on Machine Learning Algorithms
Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations
Machine-Learning-Assisted Materials Discovery from Electronic Band Structure
AMYGNN: A Graph Convolutional Neural Network-Based Approach for Predicting Amyloid Formation from Polypeptides
Alpha Shapes Applied to Molecular Shape Characterization Exhibit Novel Properties Compared to Established Shape Descriptors
CONAN (CONnectivity ANalysis): A Simple Approach in the Field of Computer-Aided Organic Synthesis. Example of the Taxane Framework
The Beilstein Handbook of Organic Chemistry: the first hundred years
Mono-Q-Polyhexes with Q Larger than 6: Polygonal Systems Representing a Class of Polycyclic Conjugated Hydrocarbons
Is Structure-Based Drug Design Ready for Selectivity Optimization?
Database Mining Using Soft Computing Techniques. An Integrated Neural Network-Fuzzy Logic-Genetic Algorithm Approach
Prediction of Material Properties from Chemical Structures. The Clearing Temperature of Nematic Liquid Crystals Derived from Their Chemical Structures by Artificial Neural Networks
Transformer-Decoder GPT Models for Generating Virtual Screening Libraries of HMG-Coenzyme A Reductase Inhibitors: Effects of Temperature, Prompt Length, and Transfer-Learning Strategies
Software Review of MNova: NMR Data Processing, Analysis, and Prediction Software
Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins
The Hydrogen Bond Environments of 1 H -Tetrazole and Tetrazolate Rings: The Structural Basis for Tetrazole-Carboxylic Acid Bioisosterism
Recommendations to Improve Text-Based Representation Systems for Polyolefins
TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories
Using Molecular Docking, 3D-QSAR, and Cluster Analysis for Screening Structurally Diverse Data Sets of Pharmacological Interest
Molecular Descriptors Influencing Melting Point and Their Role in Classification of Solid Drugs
Word Perfect Presentations 2.0 for DOS
Membrane Permeating Macrocycles: Design Guidelines from Machine Learning
Use of a maximum common subgraph algorithm in the automatic identification of ostensible bond changes occurring in chemical reactions
Steps toward the Automatic Compilation of Synthetic Organic Reactions
Evaluating the Potential of Halogen Bonding in Molecular Design: Automated Scaffold Decoration Using the New Scoring Function XBScore
Quantitatively Interpreted Enhanced Inhibition of Cytochrome P450s by Heteroaromatic Rings Containing Nitrogen
Generative Network Complex for the Automated Generation of Drug-like Molecules
Pharmacophore-Based Screening and Identification of Novel Human Ligase I Inhibitors with Potential Anticancer Activity
Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase
RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application
Automatic interpretation of the texts of chemical patent abstracts. 1. Lexical analysis and categorization
AutoDock4 Zn : An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins
Systematic Search for New Types of Chemical Interconversions: Mathematical Models and Some Applications
Docking and 3D-QSAR Studies on Isatin Sulfonamide Analogues as Caspase-3 Inhibitors
Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis
Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis"
On the Belt and Moebius Isomers of the Coronene Molecule
Computational Modeling of Kinesin Stepping
Exploring Gatekeeper Mutations in EGFR through Computer Simulations
Reactive chemical hedges: a search tool for comprehensive retrieval of chemical safety data
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking
RBNE-CMI: An Efficient Method for Predicting circRNA-miRNA Interactions via Multiattribute Incomplete Heterogeneous Network Embedding
The Black Hole Strategy: Gravity-Based Representative Sampling for Frugal Graph Learning on Metal-Organic Framework Networks
On-Line Information Systems in Perspective
Enumeration of Ring-Chain Tautomers Based on SMIRKS Rules
Chemical Information Sources: Aids in the Review of Drug Applications
Transmembrane Protein Docking with JabberDock
Pharmacophore Fingerprinting. 2. Application to Primary Library Design
Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning
Mining Discriminative Patterns from Graph Data with Multiple Labels and Its Application to Quantitative Structure-Activity Relationship (QSAR) Models
On Inactivation of the Coronavirus Main Protease
Exploiting Multiple Descriptor Sets in QSAR Studies
Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK
Molecular Shape and QSAR Analyses of a Family of Substituted Dichlorodiphenyl Aromatase Inhibitors
Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG
Substructural Analysis Techniques for Empirical Structure-Property Correlation. Application to Stereochemically Related Molecular Properties
The Detour Matrix in Chemistry
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin
Integration of Ligand and Structure Based Approaches for CSAR-2014
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation
AffiGrapher: Contrastive Heterogeneous Graph Learning with Aromatic Virtual Nodes for RNA-Small Molecule Binding Affinity Prediction
In Silico Prediction of Aqueous Solubility Using Simple QSPR Models: The Importance of Phenol and Phenol-like Moieties
Diverse Hits in De Novo Molecule Design: Diversity-Based Comparison of Goal-Directed Generators
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain
AlzyFinder: A Machine-Learning-Driven Platform for Ligand-Based Virtual Screening and Network Pharmacology
ChemCom: A Software Program for Searching and Comparing Chemical Libraries
pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors
Molecular Mechanism of D1135E-Induced Discriminated CRISPR-Cas9 PAM Recognition
Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions
Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease
TorchANI 2.0: An Extensible, High-Performance Library for the Design, Training, and Use of NN-IPs
Quantitative Prediction of Liquid Chromatography Retention of N-Benzylideneanilines Based on Quantum Chemical Parameters and Radial Basis Function Neural Network
Implementation of Quantum Machine Learning for Electronic Structure Calculations of Periodic Systems on Quantum Computing Devices
Hash Functions for Rapid Storage and Retrieval of Chemical Structures
Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification
C13Shift: a computer program for the prediction of carbon-13 NMR spectra based on an open set of additivity rules
Optimized Virtual Screening Workflow for the Identification of Novel G-Quadruplex Ligands
Fast Prediction of Lipophilicity of Organofluorine Molecules: Deep Learning-Derived Polarity Characters and Experimental Tests
Celebrating Women of Color in Computational Chemistry
TeraChem Cloud: A High-Performance Computing Service for Scalable Distributed GPU-Accelerated Electronic Structure Calculations
Techniques for Generating Descriptive Fingerprints in Combinatorial Libraries
Interpretation of Quantitative Structure-Property and -Activity Relationships
Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study
Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry
The Chemical Abstracts Service Chemical Registry System. V. Structure Input and Editing
Correction to "Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles"
Combinatorial × Computational × Cheminformatics (C 3 ) Approach to Characterization of Congeneric Libraries of Organic Pollutants
Chemoinformatics: Past, Present, and Future †
Visualization of Solar Cell Library Space by Dimensionality Reduction Methods
Electron Density Distribution in Endohedral Complexes of Fullerene C 60 , Calculated Based on the Gauss Law
Lead Finder: An Approach To Improve Accuracy of Protein-Ligand Docking, Binding Energy Estimation, and Virtual Screening
AUTONOM: system for computer translation of structural diagrams into IUPAC-compatible names. 2. Nomenclature of chains and rings
Publishing of primary information
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications
Molecular Screening and Toxicity Estimation of 260, 000 Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) through Machine Learning
Characterizing Bitterness: Identification of Key Structural Features and Development of a Classification Model
Substituent Effects on Thermochemical Properties of Free Radicals. New Substituent Scales for C-Centered Radicals
l-Arginine Binding to Human Inducible Nitric Oxide Synthase: An Antisymmetric Funnel Route toward Isoform-Specific Inhibitors?
Segment Nomenclature of Organic Compounds
Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1 Protease Complexed with Four Approved Drugs: Mechanism of Binding and Drug Resistance
Fuzzy Tricentric Pharmacophore Fingerprints. 2. Application of Topological Fuzzy Pharmacophore Triplets in Quantitative Structure-Activity Relationships
Similarity-Based Classifier Using Topomers to Provide a Knowledge Base for hERG Channel Inhibition
MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry
MCR XVI. Mathematical Support for Combinatorial Chemistry
Combination of Genetic Screening and Molecular Dynamics as a Useful Tool for Identification of Disease-Related Mutations: ZASP PDZ Domain G54S Mutation Case
Quantum Mechanical Prediction of Dissociation Constants for Thiazol-2-imine Derivatives
Modified Particle Swarm Optimization Algorithm for Adaptively Configuring Globally Optimal Classification and Regression Trees
Small Molecule Shape-Fingerprints
New Computer Aided Methods for Revealing Structural Features of Unknown Compounds Using Low Resolution Mass Spectra
An Ontology and Semantic Web Service for Quantum Chemistry Calculations
Expert system for machine-aided indexing
Impact of Polarization on the Ring Puckering Dynamics of Hexose Monosaccharides
A Classification System for Polymer Literature in an Industrial Environment
The Patent File and the Patent and Trademark Office Technology Assessment and Forecast Program
Molecular Topology Applied to the Discovery of 1-Benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2 H -pyrrole-5-one as a Non-Ligand-Binding-Pocket Antiandrogen
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions
Efficient Enumeration of Stereoisomers of Outerplanar Chemical Graphs Using Dynamic Programming
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein
Boosting Drug Discovery: Expanding the Applicability of Fragment Dissolved Molecular Dynamics to Accelerate Binding Mode Elucidation
Connectivity Network Feature Sharing in Single-Cell RNA Sequencing Data Identifies Rare Cells
SMiPoly: Generation of a Synthesizable Polymer Virtual Library Using Rule-Based Polymerization Reactions
Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy
The IFI polymer indexing system: its past, present, and future
Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network
Separation of the Energetic and Geometric Contributions to Aromaticity, 3. Analysis of the Aromatic Character of Benzene Rings in Their Various Topological and Chemical Environments in the Substituted Benzene Derivatives
MetalDock: An Open Access Docking Tool for Easy and Reproducible Docking of Metal Complexes
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery
Understanding the Enzyme ( S )-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones
QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry
Comparison of Two Methods for Predicting Aqueous Solubility
Telescoping-Solvation-Box Protocol-Based Umbrella Sampling Method for Potential Mean Force Estimation
Machine Learning Based Quantitative Structure-Dissolution Profile Relationship
A Web-Based 3D-Database Pharmacophore Searching Tool for Drug Discovery
Discovering Structural Alerts for Mutagenicity Using Stable Emerging Molecular Patterns
Detection of Constitutionally Equivalent Sites from a Connection Table
Computational Analysis of the SARS-CoV-2 RBD-ACE2-Binding Process Based on MD and the 3D-RISM Theory
Closed-shell carbon frameworks: Leapfrog fullerenes and decorated spheriphane hydrocarbons
EISA-Score: Element Interactive Surface Area Score for Protein-Ligand Binding Affinity Prediction
A Brief Recent History of Women in Computational Chemistry at Vertex Pharmaceuticals
Exhaustive Exploration of the Conformational Landscape of Small Cyclic Peptides Using a Robotics Approach
Using analytical data to build expert systems
Computer code for producing Eh-pH plots of equilibrium chemical systems
Expert Systems for Evaluating Physicochemical Property Values. 1. Aqueous Solubility
Activation/Deactivation Free-Energy Profiles for the β 2 -Adrenergic Receptor: Ligand Modes of Action
Systematic Drug Repositioning for a Wide Range of Diseases with Integrative Analyses of Phenotypic and Molecular Data
Chemical Group Theory: Techniques and Applications. Mathematical and Chemical Series, Volume 4. Edited by Danail Bonchev and Dennis H. Rouvray. Gordon and Breach Publishers, 1995, 243pp, ISBN 2-88449-034-5
Assessment of the Sampling Performance of Multiple-Copy Dynamics versus a Unique Trajectory
Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking
EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning
Electronic Conferencing on the Internet: The First Electronic Computational Chemistry Conference
Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries
Implicit Runge-Kutta method for molecular dynamics integration
Multiepitope Subunit Vaccine to Evoke Immune Response against Acute Encephalitis
Corel GALLERY 1, 000, 000, Version 3.0
Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice?
Atom pairs as molecular features in structure-activity studies: definition and applications
Generation and Selection of Novel Estrogen Receptor Ligands Using the De Novo Structure-Based Design Tool, SkelGen
Ontology Aided Modeling of Organic Reaction Mechanisms with Flexible and Fragment Based XML Markup Procedures
SmartCADD: AI-QM Empowered Drug Discovery Platform with Explainability
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method
Status of Notation and Topological Systems and Potential Future Trends
Probing the Effect of Protein and Inhibitor Conformational Flexibility on the Reaction of Rocelitinib-Like Covalent Inhibitors of Epidermal Growth Factor Receptor. A Quantum Mechanics/Molecular Mechanics Study
Structural Features of Toxic Chemicals for Specific Toxicity
Exploring Protein-Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches
Hazards in Factor Analysis
An Ontology for Pharmaceutical Ligands and Its Application for in Silico Screening and Library Design
Computational Chemistry Using the PC. By Donald W. Rogers. VCH: New York, 1994, 247 pp, ISBN 1-56081-672-4
AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening
Evaluating the Use of Graph Neural Networks and Transfer Learning for Oral Bioavailability Prediction
Structural Determination of (Al 2 O 3 ) n ( n = 1-15) Clusters Based on Graphic Processing Unit
Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies
Chemical and Biological Properties of Frequent Screening Hits
Machine Learning-Assisted Carbon Dot Synthesis: Prediction of Emission Color and Wavelength
A Probabilistic Derivation of the Partial Least-Squares Algorithm
Molecular Insights into the Substrate-Assisted Mechanism of Viral DNA 3′-End Processing in Intasome of Prototype Foamy Virus Integrase from Molecular Dynamic and QM/MM Studies
COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework
Studies of Patterns and Statistical Trends in a Database of Inorganic Chemical Reactions-Some Interesting Observations on Stoichiometry
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies
Speeding Up a Genetic Algorithm for EPR-Based Spin Label Characterization of Biosystem Complexity
Feature Selection for Descriptor Based Classification Models. 2. Human Intestinal Absorption (HIA)
Discovery of Wild-Type and Y181C Mutant Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors Using Virtual Screening with Multiple Protein Structures
Composition and Topology of Activity Cliff Clusters Formed by Bioactive Compounds
Torsion Angle Preference and Energetics of Small-Molecule Ligands Bound to Proteins
Hamilton Cycles and Paths in Fullerenes
Algorithm for Advanced Canonical Coding of Planar Chemical Structures That Considers Stereochemical and Symmetric Information
Chemical Abstracts coverage of the preclinical sciences journal literature
Microlevel Infometric Investigation in Phytochemistry
Combatting Antibiotic-Resistant Staphylococcus aureus : Discovery of TST1N-224, a Potent Inhibitor Targeting Response Regulator VraRC, through Pharmacophore-Based Screening and Molecular Characterizations
Intuitive Patent Markush Structure Visualization Tool for Medicinal Chemists
Optimal Replica-Exchange Molecular Simulations in Combination with Evolution Strategies
Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and compatibility
Protein-Peptide Binding Site Detection Using 3D Convolutional Neural Networks
Random walks: computations and applications to chemistry
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry
Development and Validation of an Automated DNA-Encoded Library Screening Data Analysis Platform: PB-DEL Autoscreening Analysis (PB-DELASA)
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion
Explicit Diversity Index (EDI): A Novel Measure for Assessing the Diversity of Compound Databases
Identification of Protein-Protein Interactions by Detecting Correlated Mutation at the Interface
Preprocessing of Single Cell RNA Sequencing Data Using Correlated Clustering and Projection
Dynamic View of Allosteric Regulation in the Hsp70 Chaperones by J-Domain Cochaperone and Post-Translational Modifications: Computational Analysis of Hsp70 Mechanisms by Exploring Conformational Landscapes and Residue Interaction Networks
Application of a Feed-Forward Artificial Neural Network as a Mapping Device
Update to Our Reader, Reviewer, and Author Communities - April 2020
Role of Water in the Puzzling Mechanism of the Final Aromatization Step Promoted by the Human Aromatase Enzyme. Insights from QM/MM MD Simulations
Pagemaker
Markov Logic Networks for Optical Chemical Structure Recognition
Three-Dimensional Quantitative Structure-Permeability Relationship Analysis for a Series of Inhibitors of Rhinovirus Replication
Deep Learning with Geometry-Enhanced Molecular Representation for Augmentation of Large-Scale Docking-Based Virtual Screening
RLMolLM: Reinforcement Learning-Enhanced Language Model Framework for Inverse Molecular Design
ProSECFPs: A Novel Fingerprint-Based Protein Representation Method for Missense Mutation Pathogenicity Prediction
Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics
The generation of reaction networks with RAIN. 1. The reaction generator
Structural Characterization of the Molecular Dimer of the Peptide Antibiotic Vancomycin by Distance Geometry in Four Spatial Dimensions
A Guide to Biomolecular Simulations By Oren M. Becker and Martin Karplus. Series: Focus on Structural Biology; Springer, Dordrecht, 2006. Vol 4, 220 pp. ISBN 1-4020-3586-1. Hardcover U.S. $89.95, Euro74.95
Quantitative Antidiabetic Activity Prediction for the Class of Guanidino- and Aminoguanidinopropionic Acid Analogs Based on Electron-Conformational Studies
Cost-effective operation for an agricultural information center
Predictive Models for Aquatic Toxicity of Aldehydes Designed for Various Model Chemistries
Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: the Main Protease (Mpro) Case Study
Similarity approach to chemical reactivity. A simple criterion for discriminating between one-step and stepwise reaction mechanisms in pericyclic reactivity
Prompt-CBP: A Novel Prompt Learning-Based Model for Predicting Cross-Species Promoters
Application of Computer-Aided Drug Repurposing in the Search of New Cruzipain Inhibitors: Discovery of Amiodarone and Bromocriptine Inhibitory Effects
Clustering multidisciplinary chemical papers to provide new tools for research management and trends. Application to coal and organic matter oxidation
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies
Computer algebra in chemistry
Enzyme Binding Selectivity Prediction: alpha-Thrombin vs Trypsin Inhibition
Computational Insights into Molecular Activation and Positive Cooperative Mechanisms of FFAR1 Modulators
Non-Canonical Interaction between Calmodulin and Calcineurin Contributes to the Differential Regulation of Plant-Derived Calmodulins on Calcineurin
Surfing the Organic Chemistry Hyperdocument with CrossFire plus Reactions1
Application of standard robotic methods to water analysis
Single-resonance subspectra/substructure investigations of the carbon-13 DARC databank. Representation of local and global topological knowledge
OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods
Accelerating Prediction of Antiviral Peptides Using Genetic Algorithm-Based Weighted Multiperspective Descriptors with Self-Normalized Deep Networks
Toward a Principled Methodology for Neural Network Design and Performance Evaluation in QSAR. Application to the Prediction of LogP