yusuke1997/dblp-id-title huggingface dataset:
Conformational Analysis of Heparin-Analogue Pentasaccharides by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulations
Analog Accessibility Score (AAscore) for Rational Compound Selection
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons
Using Symbolic Problems in Teaching Chemistry
CPIScore: A Deep Learning Approach for Rapid Scoring and Interpretation of Protein-Ligand Binding Interactions
Peptide-Tools-Web Server for Calculating Physicochemical Properties of Peptides
PMechDB: A Public Database of Elementary Polar Reaction Steps
Stability of Prediction in Production ADMET Models as a Function of Version: Why and When Predictions Change
Graph automorphism perception algorithms in computer-enhanced structure elucidation
New Discoveries in Hybrid Orbitals to Characterize Molecules and Predict Biomolecular Interactions
Evolving Mutational Buildup in HIV-1 Protease Shifts Conformational Dynamics to Gain Drug Resistance
Dynamic Structure of NGF and proNGF Complexed with p75NTR: Pro-Peptide Effect
Prediction of the Brain-Blood Distribution of a Large Set of Drugs from Structurally Derived Descriptors Using Partial Least-Squares (PLS) Modeling
Molecular Modeling Studies Focused on 5-HT 7 versus 5-HT 1A Selectivity. Discovery of Novel Phenylpyrrole Derivatives with High Affinity for 5-HT 7 Receptors
Discovery of Novel Small-Molecule Calcium Sensitizers for Cardiac Troponin C: A Combined Virtual and Experimental Screening Approach
Graph-Based Chemical Nomenclature. 1. Historical Background and Discussion
High-Throughput Molecular Design of Donors and Non-Fullerene Acceptors for Organic Solar Cells Based on Convolutional Neural Networks
Identification of Protein-Ligand Binding Sites by Sequence Information and Ensemble Classifier
Electronic Chemistry Conferences: 7 Years of CONFCHEM
Construction and Validation of a RET TK Catalytic Domain by Homology Modeling
A Study of Computer-Based Current Awareness Bulletins-UKCIS Macroprofiles
Two New Parameters Based on Distances in a Receiver Operating Characteristic Chart for the Selection of Classification Models
Improved Prediction of Drug-Target Interactions Using Self-Paced Learning with Collaborative Matrix Factorization
HBCalculator: A Tool for Hydrogen Bond Distribution Calculations in Molecular Dynamics Simulations
Understanding the Origin of Enhanced Piezoelectric Response in PVDF Matrices with Embedded ZnO Nanoparticles, from Polarizable Molecular Dynamics Simulations
Understanding the Structure and Apo Dynamics of the Functionally Active JIP1 Fragment
Multitarget Structure-Activity Relationships Characterized by Activity-Difference Maps and Consensus Similarity Measure
Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained
Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes
Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape
NBCR-ac4C: A Deep Learning Framework Based on Multivariate BERT for Human mRNA N4-Acetylcytidine Sites Prediction
AntiBac-Pred: A Web Application for Predicting Antibacterial Activity of Chemical Compounds
Linear Indices of the "Molecular Pseudograph's Atom Adjacency Matrix": Definition, Significance-Interpretation, and Application to QSAR Analysis of Flavone Derivatives as HIV-1 Integrase Inhibitors
AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors
Computational Design of Lysine Targeting Covalent Binders Using Rosetta
SMIREP: Predicting Chemical Activity from SMILES
Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs
Simulated Annealing Construction of Molecular Graphs with Required Properties
Discovering New Acetylcholinesterase Inhibitors by Mining the Buzhongyiqi Decoction Recipe Data
Emerging Dominant SARS-CoV-2 Variants
COMPAS-4: A Data Set of (BN) 1 Substituted Cata -Condensed Polybenzenoid Hydrocarbons─Data Analysis and Feature Engineering
Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations
Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics
Structural Diversity of Small Molecule Libraries
Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug-Target Interaction Prediction
MolHyb: A Web Server for Structure-Based Drug Design by Molecular Hybridization
Identification of Inhibitors against p90 Ribosomal S6 Kinase 2 (RSK2) through Structure-Based Virtual Screening with the Inhibitor-Constrained Refined Homology Model
Sources of Chemical Information Used in Antibiotic Certification
Comparison of Weighting Schemes for Molecular Graph Descriptors: Application in Quantitative Structure-Retention Relationship Models for Alkylphenols in Gas-Liquid Chromatography
Enumeration of Conjugated Circuits in Nanotubes
Algorithms for the computation of molecular distance matrix and distance polynomial of chemical graphs on parallel computers
Mapping the Molecular Architecture Required for Lipid-Binding Pockets Using a Subset of Established and Orphan G-Protein Coupled Receptors
Conformational Sampling by Self-Organization
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease
Quantitative Analysis of Dynamic Allostery
PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization
Subductive and inductive derivation for designing molecules of high symmetry
Data-Based Prediction of Redox Potentials via Introducing Chemical Features into the Transformer Architecture
Prediction of Aqueous Solubility of Organic Compounds Based on a 3D Structure Representation
EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation
Identification of a Novel Structural Class of H V 1 Inhibitors by Structure-Based Virtual Screening
Exploration of the Parameter Space of an Ion Channel Kinetic Model by a Markov-Chain-Based Methodology
Enhancing the Sensitivity of Pharmacophore-Based Virtual Screening by Incorporating Customized ZBG Features: A Case Study Using Histone Deacetylase 8
Discovery of Targeted Covalent Natural Products against PLK1 by Herb-Based Screening
Compact numeric alkane codes derived from IUPAC nomenclature
Molecule Property Prediction Based on Spatial Graph Embedding
State-Specific Peptide Design Targeting G Protein-Coupled Receptors
Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations
Definition and role of similarity concepts in the chemical and physical sciences
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
Three Methods for Calculation of the Hyper-Wiener Index of Molecular Graphs
Authentication of Internet-Based Distributed Computing Resources in Chemistry
Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores
A Contribution to the Drug Resistance Mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir Complexes with HIV-1 Protease Due to Flap Mutation I50V: A Systematic MM-PBSA and Thermodynamic Integration Study
MOLDYN: a generalized program for the evaluation of molecular dynamics models using nuclear magnetic resonance spin-relaxation data
Computational Investigation of Ligand Binding to the Peripheral Site in CYP3A4: Conformational Dynamics and Inhibitor Discovery
A 3D-QSAR Study of Anticoccidial Triazines Using Molecular Shape Analysis [J. Chem. Inf. Comput. Sci 35, 771-778 (1995)]
Topological Indices and Related Descriptors in QSAR and QSPR Edited by James Devillers & Alexandru T. Balaban. Gordon and Breach Science Publishers: Singapore, 1999, 811 pp, ISBN 90-5699-239-2
Comparative Performance of High-Throughput Methods for Protein p K a Predictions
Drug-like Index: A New Approach To Measure Drug-like Compounds and Their Diversity
The Block Copolymer Phase Behavior Database
Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
Addressing Selective Polypharmacology of Antipsychotic Drugs Targeting the Bioaminergic Receptors through Receptor Dynamic Conformational Ensembles
Thermodynamic implications of substituent and solvent effects on reactivity
EvaluationMaster: A GUI Tool for Structure-Based Virtual Screening Evaluation Analysis and Decision-Making Support
Computer simulation of physical-chemical properties of organic molecules. 1. Molecular system identification
Detection and Classification of Organophosphate Nerve Agent Simulants Using Support Vector Machines with Multiarray Sensors
Improving Virtual Screening Performance against Conformational Variations of Receptors by Shape Matching with Ligand Binding Pocket
Docking-Based Comparative Intermolecular Contacts Analysis as New 3-D QSAR Concept for Validating Docking Studies and in Silico Screening: NMT and GP Inhibitors as Case Studies
Using High-Throughput Screening Data To Discriminate Compounds with Single-Target Effects from Those with Side Effects
Prediction of Normal Boiling Points for a Diverse Set of Industrially Important Organic Compounds from Molecular Structure
SGcCA: Deciphering Drug-Target Interactions through an End-to-End Model with Spatial and Channel Reconstruction Convolution and Cross-Efficient-Additive Attention
Comprehensive Evaluation of End-Point Free Energy Methods in DNA-Ligand Interaction Predictions
Correction to "Machine Learning for Sequence and Structure-Based Protein-Ligand Interaction Prediction"
GRID Formalism for the Comparative Molecular Surface Analysis: Application to the CoMFA Benchmark Steroids, Azo Dyes, and HEPT Derivatives
Compare Conformer: a program for the rapid comparison of molecular conformers based on interatomic distances and torsion angles
Dihedral-Based Segment Identification and Classification of Biopolymers I: Proteins
Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces
ChemPlus for Windows
Novel Models for Accurate Estimation of Air-Blood Partitioning: Applications to Individual Compounds and Complex Mixtures of Neutral Organic Compounds
Historical Aspects of Patent Systems
Assessing the Protective Activity of a Recently Discovered Phenolic Compound against Oxidative Stress Using Computational Chemistry
Quantitative Structure-Activity Relationships of the Synthetic Substrates for Elastase Enzyme Using Nonlinear Partial Least Squares Regression
On the Microtubule-Stabilizing Properties of a Tau Oligopeptide
ProSTAGE: Predicting Effects of Mutations on Protein Stability by Using Protein Embeddings and Graph Convolutional Networks
Detailed Mechanism Generation. 1. Generalized Reactive Properties as Reaction Class Substructures
Feasibility of Active Machine Learning for Multiclass Compound Classification
Electrostatic potential derived charges for enzyme cofactors: methods, correlations, and scaling for organic cofactors
Efficient In Silico Saturation Mutagenesis of a Member of the Caspase Protease Family
Design of Libraries To Explore Receptor Sites
ResiDEM: Analytical Tool for Isomorphous Difference Electron Density Maps Utilizing Dynamic Residue Identification via Density Clustering
Optimization of Functional Group Prediction from Infrared Spectra Using Neural Networks
Structured biological data in the molecular access system
Application of Genetic Function Approximation to Quantitative Structure-Activity Relationships and Quantitative Structure-Property Relationships
Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics
Perturbation Theory-Machine Learning Study of Zeolite Materials Desilication
Making "Real" Molecules in Virtual Space
Leveraging DFT and Molecular Fragmentation for Chemically Accurate p K a Prediction Using Machine Learning
QSAR Modeling with the Electrotopological State: TIBO Derivatives
Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity
EChem++-An Object-Oriented Problem Solving Environment for Electrochemistry. 2. The Kinetic Facilities of Ecco-A Compiler for (Electro-)Chemistry
Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization
Proteomic Maps-Toxicity Relationship of Halocarbons Studied with Similarity Index and Genetic Algorithm
Confronting Racism in Chemistry Journals
The hpCADD NDDO Hamiltonian: Parametrization
PoseidonQ: A Free Machine Learning Platform for the Development, Analysis, and Validation of Efficient and Portable QSAR Models for Drug Discovery
gSelformer-MV: Multiview, Subgraph-Augmented Group SELFIES Transformer for Molecular Property Prediction
CD-ROM chemical databases: The influence of data structure and graphical user interfaces on information access
PowerMV: A Software Environment for Molecular Viewing, Descriptor Generation, Data Analysis and Hit Evaluation
Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces
Computational Chemistry in the Global South: A Latin American Perspective
Deep Learning-Driven Insights into Enzyme-Substrate Interaction Discovery
Emerging Landscape of Computational Modeling in Pharmaceutical Development
Fast Similarity Search in Three-Dimensional Structure Databases
Correlations between chemical structure and normal boiling points of halogenated alkanes C1-C4
Caught in a CrossFire: Academic Libraries and Beilstein
Development of a Rule-Based Method for the Assessment of Protein Druggability
Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps
ANABAG: Annotated Antibody-Antigen Data Set with Unique Features for Antibody Engineering Applications
High-Throughput Screening Approach for the Optoelectronic Properties of Conjugated Polymers
Stochastic Pairwise Alignments and Scoring Methods for Comparative Protein Structure Modeling
Patent coverage by abstracting services. 4. Coverage of microbiological patents
Value of the Urinary Stone Promoters/Inhibitors Ratios in the Estimation of the Risk of Urolithiasis
Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs
Halogen Bond: Its Role beyond Drug-Target Binding Affinity for Drug Discovery and Development
mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets
Structural Insights into the Ligand Binding Domain of the Glucocorticoid Receptor: A Molecular Dynamics Study
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction
Ensemble Docking Approach to Mitigate Pregnane X Receptor-Mediated CYP3A4 Induction Risk
Truncated Arctangent Rank Minimization and Double-Strategy Neighborhood Constraint Graph Inference for Drug-Disease Association Prediction
3D-QSAR CoMFA of a Series of DABO Derivatives as HIV-1 Reverse Transcriptase Non-Nucleoside Inhibitors
Identifying Promising Compounds in Drug Discovery: Genetic Algorithms and Some New Statistical Techniques
Rapid Automated Quantification of Triacylglyceride Crystallinity in Molecular Dynamics Simulations
Combining AlphaFold with Focused Virtual Library Design in the Development of Novel CCR2 and CCR5 Antagonists
Structural Assessment of Agonist Efficacy in the μ-Opioid Receptor: Morphine and Fentanyl Elicit Different Activation Patterns
Enhanced Structure Elucidation
How Does Catalase Release Nitric Oxide? A Computational Structure-Activity Relationship Study
Computer translation of IUPAC systematic organic chemical nomenclature. 1. Introduction and background to a grammar-based approach
Matrix Operator, W(M1, M2, M3), and Schultz-Type Indices
DNA Solution of a Graph Coloring Problem
Evaluation of a Semi-Automated Workflow for Fragment Growing
Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark
Influence and Interrelationship of Chemical Journals
Similarity Perception of Reactions Catalyzed by Oxidoreductases and Hydrolases Using Different Classification Methods
Editorial: Method and Data Sharing and Reproducibility of Scientific Results
Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design
Rational Design Based on Bioactive Conformation Analysis of Pyrimidinylbenzoates as Acetohydroxyacid Synthase Inhibitors by Integrating Molecular Docking, CoMFA, CoMSIA, and DFT Calculations
Optimal Descriptor Subset Search via Chemical Information and Target Activity-Guided Algorithm for Antimicrobial Peptide Prediction
Citation Analysis, Mechanical Translation of Chemical Nomenclature, and the Macrostructure of Science
Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening
Determination of Structural Ensembles of Flexible Molecules in Solution from NMR Data Undergoing Spin Diffusion
Median Partitioning: A Novel Method for the Selection of Representative Subsets from Large Compound Pools
Production of a Comprehensive Research Directory from Multiple Secondary Sources
Representing Polymers as Periodic Graphs with Learned Descriptors for Accurate Polymer Property Predictions
Step-by-Step Calculation of All Maximum Common Substructures through a Constraint Satisfaction Based Algorithm
Comparisons of Molecular Structure Generation Methods Based on Fragment Assemblies and Genetic Graphs
Prediction of Membrane Protein Types by Incorporating Amphipathic Effects
PAZ Domain Pivoting is the Rate-Limiting Step for Target DNA Recognition in the Middle Region of Thermus thermophilus Argonaute
Neural Network Prediction of Carbon-13 NMR Chemical Shifts of Alkanes
E-Novo : An Automated Workflow for Efficient Structure-Based Lead Optimization
Selecting Combinatorial Libraries to Optimize Diversity and Physical Properties
Employing Artificial Neural Networks for Optimal Storage and Facile Sharing of Molecular Dynamics Simulation Trajectories
Predicting Reaction Products and Automating Reactive Trajectory Characterization in Molecular Simulations with Support Vector Machines
A Survey of the Use of On-Line Computer-Based Scientific Search Services by Academic Libraries
Computational Models for the Helix Tilt Angle
In Silico Deconstruction of ATP-Competitive Inhibitors of Glycogen Synthase Kinase-3β
Applications of graph theory in chemistry
RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4
A Computational Investigation of Small-Molecule Engagement of Hot Spots at Protein-Protein Interaction Interfaces
Canonical Numbering and Constitutional Symmetry
Graph potentials method and its application for chemical information processing
Divergent Spatiotemporal Interaction of Angiotensin Receptor Blocking Drugs with Angiotensin Type 1 Receptor
DOVE, a Rational Analysis of Sparse Data
Searching the Chemical Abstracts Condensates Data Base via Two On-Line Systems
MechBERT: Language Models for Extracting Chemical and Property Relationships about Mechanical Stress and Strain
In Silico Design and Analysis of a Kinase-Focused Combinatorial Library Considering Diversity and Quality
Pharmacophore Fingerprinting. 1. Application to QSAR and Focused Library Design
Q-raKtion: A Semiautomated KNIME Workflow for Bioactivity Data Points Curation
Draft specification for revised version of the Standard Molecular Data (SMD) Format
Iodide Binding in Sodium-Coupled Cotransporters
Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS)
Combinatorial Enumeration of Nonrigid Isomers with Given Ligand Symmetries on the Basis of Promolecules with A Subsymmetry of Dh
2D and 3D Quantitative Structure-Activity Relationship Study of Hepatitis C Virus NS5B Polymerase Inhibitors by Comparative Molecular Field Analysis and Comparative Molecular Similarity Indices Analysis Methods
The Application of Chemical Multipurpose Internet Mail Extensions (Chemical MIME) Internet Standards to Electronic Mail and World Wide Web Information Exchange
The Complexity of Parallel Symplectic Molecular Dynamics Algorithms
Experimental system for similarity and 3D searching of CAS registry substances. 1. 3D substructure searching
Notes on isocodal graphs
Rule-Based System To Derive Automatically Good-List and Bad-List Entries for Structure Generators from Spectra
In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers
Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs
Searching for simple generic structures
Overcoming the Limitations of a Connection Table Description: A Universal Representation of Chemical Species
Effect of Stapling on the Thermodynamics of mdm2-p53 Binding
On Heteroaromaticity of Nucleobases. Bond Lengths as Multidimensional Phenomena
Which Three-Dimensional Characteristics Make Efficient Inhibitors of Protein-Protein Interactions?
Torsional Energy Barriers of Biaryls Could Be Predicted by Electron Richness/Deficiency of Aromatic Rings; Advancement of Molecular Mechanics toward Atom-Type Independence
ProtSqueeze: Simple and Effective Automated Tool for Setting up Membrane Protein Simulations
A Comparative Report on an On-Line Retrieval Service Employing Two Distinct Software Systems
Common Pharmacophore Identification Using Frequent Clique Detection Algorithm
Question Answering System for Chemistry
Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations
Essentials of Computational Chemistry, Theories and Models By Christopher J. Cramer. Wiley 2002, ISBN 0-471-48551-9
Genetic Programming for the Induction of Decision Trees to Model Ecotoxicity Data
MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network
LGABAN: An Integrated Multi-Scale Approach Combining Graph and Sequence Features for Enhanced Prediction of Drug-Protein Interactions
Database retrieval techniques for carbon-13 nuclear magnetic resonance spectrum simulation
Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors
A Novel Automated Lazy Learning QSAR (ALL-QSAR) Approach: Method Development, Applications, and Virtual Screening of Chemical Databases Using Validated ALL-QSAR Models
The Role of Ribose Modifications on the Structural Stability of Nucleotide Analogues with α-Thiotriphosphate at the Active Site of SARS-CoV-2 RdRp
Identification of Potent ADCK3 Inhibitors through Structure-Based Virtual Screening
Leveraging-Induced Polarization for Drug Discovery: Efficient IC50 Prediction Using Minimal Features
Recursive Distance Partitioning Algorithm for Common Pharmacophore Identification
Molecular Dynamics Perspective on the Protein Thermal Stability: A Case Study Using SAICAR Synthetase
Effect of Molecular Descriptor Feature Selection in Support Vector Machine Classification of Pharmacokinetic and Toxicological Properties of Chemical Agents
Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C
CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis
Off-Line Input of Chemical Structures with a Low-Cost Microprocessor-Controlled Semigraphical CRT
BRICS-Based Generation and AI-Assisted Screening of Ionic Liquids with Mechanistic Insights into Lithium Transport in Electrolytes
Target-Specific De Novo Peptide Binder Design with DiffPepBuilder
CHUCKLES: A method for representing and searching peptide and peptoid sequences on both monomer and atomic levels
Coping with Unbalanced Class Data Sets in Oral Absorption Models
GISAXS View of Vanadium/Cerium Oxide Thin Films and Influence of Lithium Intercalation
Circuit Topology Approach for the Comparative Analysis of Intrinsically Disordered Proteins