yusuke1997/dblp-id-title huggingface dataset:
Clustering Chemical Databases Using Adaptable Projection Cells and MCS Similarity Values
Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules
Exploring the Potential of Adaptive, Local Machine Learning in Comparison to the Prediction Performance of Global Models: A Case Study from Bayer's Caco-2 Permeability Database
Multiscale Computational Dissection of CCRL2-Mediated Chemerin Presentation
Algorithms for Unique and Unambiguous Coding and Symmetry Perception of Molecular Structure Diagram. I. Vector Function for Automorphism Partitioning
Moss-m7G: A Motif-Based Interpretable Deep Learning Method for RNA N7-Methlguanosine Site Prediction
Identifying Novel Molecular Structures for Advanced Melanoma by Ligand-Based Virtual Screening
Prediction of Activity and Selectivity Profiles of Sigma Receptor Ligands Using Machine Learning Approaches
ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations
Four Association Coefficients for Relating Molecular Similarity Measures
Development of Neural Network Simulator for Structure-Activity Correlation of Molecules (NECO). Prediction of Endo/Exo Substitution of Norbornane Derivatives and of Carcinogenic Activity of PAHs from 13C-NMR Shifts
Comparison of Ranking Methods for Virtual Screening in Lead-Discovery Programs
MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies
Chemical Structure and Superconductivity
Bioactive Diversity and Screening Library Selection via Affinity Fingerprinting
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism
Simple stereochemical structure code for organic chemistry
Correction to "NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit"
Stochastic Similarity Selections from Large Combinatorial Libraries
Topological considerations subtly inherent in the formulation and subdivision of fused vs. bridged ring compounds
Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic
Inorganic Materials Synthesis Planning with Literature-Trained Neural Networks
A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins
Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval
Quantum Mechanical Structure-Activity Relationship Analyses for Skin Sensitization
Book Review of Apple Pro Training Series: Motion 3
Personal microcomputer based system of chemical information with topological structure data elaboration
Discovery of Novel Phosphodiesterase-2A Inhibitors by Structure-Based Virtual Screening, Structural Optimization, and Bioassay
Structural similarity searching using descriptors developed for structure-activity relationship studies
Structure Prediction of Alternate Frame Folding Systems with AlphaFold3
Toward a Structural View of hERG Activation by the Small-Molecule Activator ICA-105574
Structure Based Design, Synthesis, Pharmacophore Modeling, Virtual Screening, and Molecular Docking Studies for Identification of Novel Cyclophilin D Inhibitors
Docking Ligands into Flexible and Solvated Macromolecules, 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy
Structure-Related Statistical Singularities along Protein Sequences: A Correlation Study
ChargeNet: E(3) Equivariant Graph Attention Network for Atomic Charge Prediction
QSPR Treatment of the Unified Nonspecific Solvent Polarity Scale
Rethinking Retrosynthesis: Curriculum Learning Reshapes Transformer-Based Small-Molecule Reaction Prediction
Machine-Learning-Based Predictive Modeling of Glass Transition Temperatures: A Case of Polyhydroxyalkanoate Homopolymers and Copolymers
What Is the Smallest Saturated Acyclic Alkane that Cannot Be Made?
Prediction of 1 H NMR Coupling Constants with Associative Neural Networks Trained for Chemical Shifts
From Molecular to Biological Structure and Back
Allosteric Cooperativity Mechanism Investigation of Orthosteric and Allosteric Ligands in Modulating AR Activity: A Molecular Dynamics Study
Molecular Design Based on 3D-Pharmacophore. Application to 5-HT Subtypes Receptors
Head-to-Tail Cyclization Enhances Ice-Growth Inhibition by Linear Threonine Oligomers
Automating Knowledge Discovery for Toxicity Prediction Using Jumping Emerging Pattern Mining
Postprocessing of Protein-Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors
Artificial Neural Networks and Linear Discriminant Analysis: A Valuable Combination in the Selection of New Antibacterial Compounds
De Novo Design of Multitarget Ligands with an Iterative Fragment-Growing Strategy
Identification of Anticancer Peptides from the Genome of Candida albicans : in Silico Screening, in Vitro and in Vivo Validations
Theory of Correlation Tables, 2
Virtual Screening Using Binary Kernel Discrimination: Effect of Noisy Training Data and the Optimization of Performance
Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments
Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and graph theory
Some observations on piecemeal electronic publishing solutions in the pharmaceutical industry
ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands [ J. Chem. Inf. Model, 47 , 425-434 (2007)]
Distance-Related Indexes in the Quantitative Structure-Property Relationship Modeling
Transformation of Harmonics for Molecular Calculations
Target Family-Directed Exploration of Scaffolds with Different SAR Profiles
Computer Software Reviews-Aztec C Compiler for the Macintosh
Chemical Space Networks Enhance Toxicity Recognition via Graph Embedding
Input Pose is Key to Performance of Free Energy Perturbation: Benchmarking with Monoacylglycerol Lipase
Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition
Boiling Point and Critical Temperature of a Heterogeneous Data Set: QSAR with Atom Type Electrotopological State Indices Using Artificial Neural Networks
Historic development of chemical notations
Synthesis-Aware Generation of Structural Analogues
Heat Capacity of Ionic Liquids: Toward Interpretable Chemical Structure-Based Machine Learning Approaches
Benchmarks of the PC-UNIX Computer with Electronic Structure Calculation
Unraveling the Disruptive Mechanism of Local Anesthetics on Raft-Like Ordered Membranes: Simulation Studies
Perplexity-Based Molecule Ranking and Bias Estimation of Chemical Language Models
SHED: Shannon Entropy Descriptors from Topological Feature Distributions
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
A Celebration of Women in Computational Chemistry
Mining and Visualizing Large Anticancer Drug Discovery Databases
Multiclass Synthetic Accessibility Prediction
Spectral Pattern Recognition Using Self-Organizing MAPS
Prediction of Protein Allosteric Sites with Transfer Entropy and Spatial Neighbor-Based Evolutionary Information Learned by an Ensemble Model
Formula Periodic Tables-Their Construction and Related Symmetries
Evaluating Hydrogen Bonds and Base Stacking of Single, Tandem and Terminal GU Mismatches in RNA with a Mesoscopic Model
Electronic Coupling Effects on Photoinduced Electron Transfer in Carotene-Porphyrin-Fullerene Triads Detected by Time-Resolved EPR
Converting SMILES to Stacking Interaction Energies
Identifying Potent Compounds Using Pairwise Consensus Methods
Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA
Cross-Docking of Inhibitors into CDK2 Structures. 1
QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase
Insights from Fragment Hit Binding Assays by Molecular Simulations
Estimation of Aqueous Solubility of Chemical Compounds Using E-State Indices
Multilabel Classification Models for the Prediction of Cross-Coupling Reaction Conditions
Chirality Effects in Biomolecular Systems: Calculation of the Relative Free Energies by Molecular Dynamics Simulations
Use of Recursion Forests in the Sequential Screening Process: Consensus Selection by Multiple Recursion Trees
The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR Studies
Dihedral-Based Segment Identification and Classification of Biopolymers II: Polynucleotides
Using Bibliometric Analyses of Patent Literature for Predicting the Clinical Fates of Developing Drugs
Structure/Response Correlations and Similarity/Diversity Analysis by GETAWAY Descriptors, 2. Application of the Novel 3D Molecular Descriptors to QSAR/QSPR Studies
logD 7.4 Modeling Using Bayesian Regularized Neural Networks. Assessment and Correction of the Errors of Prediction
Data-Driven Prediction of Structures of Metal-Organic Frameworks
A Novel Automated Framework for QSAR Modeling of Highly Imbalanced Leishmania High-Throughput Screening Data
FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks
Wiener Numbers of Phenylenes: An Exact Result
Modeling the Binding and Conformational Energetics of a Targeted Covalent Inhibitor to Bruton's Tyrosine Kinase
Mechanistic Insights into the Reversible Inhibition of d-Cycloserine in Alanine Racemase from Mycobacterium tuberculosis
Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials
Compression of Wiswesser Line Notations Using Variety Generation
AisNet: A Universal Interatomic Potential Neural Network with Encoded Local Environment Features
Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling
Chemical Abstracts ONLINE: a study of the quality of controlled terms
CalcUS: An Open-Source Quantum Chemistry Web Platform
Multi-CGAN: Deep Generative Model-Based Multiproperty Antimicrobial Peptide Design
Advances in Machine Learning Models for Predicting Enzyme Kinetic Parameters
Catalytic Mechanism and Covalent Inhibition of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA): Implications to the Design of Novel Antibacterials
Integrating Machine Learning-Based Pose Sampling with Established Scoring Functions for Virtual Screening
Apo2ph4 : A Versatile Workflow for the Generation of Receptor-based Pharmacophore Models for Virtual Screening
An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations
Several New Diverse Anticonvulsant Agents Discovered in a Virtual Screening Campaign Aimed at Novel Antiepileptic Drugs to Treat Refractory Epilepsy
Systematic Identification and Classification of Three-Dimensional Activity Cliffs
MSLDOCK: Multi-Swarm Optimization for Flexible Ligand Docking and Virtual Screening
Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design
Combining QM/MM Calculations with Classical Mining Minima to Predict Protein-Ligand Binding Free Energy
Enhanced CACTVS Browser of the Open NCI Database
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta
An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling
Learning system for automatic structural analysis of mass spectra
BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations
Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries
Effects of Single Nucleotide Polymorphisms on the Binding of Afatinib to EGFR: A Potential Patient Stratification Factor Revealed by Modeling Studies
Modeling of Cyclin-Dependent Kinase Inhibition by 1 H -Pyrazolo[3, 4- d ]Pyrimidine Derivatives Using Artificial Neural Network Ensembles
Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation
CAT: A Compound Attachment Tool for the Construction of Composite Chemical Compounds
On the Basis of Invariants of Labeled Molecular Graphs
Symantec Norton Antivirus 2.0 for Windows 95
Crystallographic studies of inter- and intramolecular interactions reflected in aromatic character of .pi.-electron systems
Prediction of the Isoelectric Point of an Amino Acid Based on GA-PLS and SVMs
Introducing Uncertainty in Predictive Modeling - Friend or Foe?
Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity
Ligand Prediction from Protein Sequence and Small Molecule Information Using Support Vector Machines and Fingerprint Descriptors
Dynamic Insights into the Self-Activation Pathway and Allosteric Regulation of the Orphan G-Protein-Coupled Receptor GPR52
Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles
Journal of Chemical Information and Modeling
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism
Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach
The Physical Driving Forces of Conformational Transition for TTR 91-96 with Proline Mutations
An Efficient Symplectic Integration Algorithm for Molecular Dynamics Simulations
A novel algorithm for local minimum escape in back-propagation neural networks: application to the interpretation of matrix isolation infrared spectra
Characteristic Monomials with Chirality Fittingness for Combinatorial Enumeration of Isomers with Chiral and Achiral Ligands
Helium 4 Dimer in Nanotubes
Density Functional Theory and Electrochemical Studies: Structure-Efficiency Relationship on Corrosion Inhibition
Understanding the Impact of the P-loop Conformation on Kinase Selectivity
Volatile Anesthetic Binding to Proteins Is Influenced by Solvent and Aliphatic Residues
ezCADD: A Rapid 2D/3D Visualization-Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design
Omicron Binding Mode: Contact Analysis and Dynamics of the Omicron Receptor-Binding Domain in Complex with ACE2
Quantum Molecular Similarity. 3. QTMS Descriptors
Robust Prediction of Protein-Ligand Binding Potency with Multi-modal Customized Gate Control
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics
Modeling Compound-Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design
Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics
Self-Association of ACE-2 with Different RBD Amounts: A Dynamic Simulation Perspective on SARS-CoV-2 Infection
Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field
Inverse problem in QSAR/QSPR studies for the case of topological indexes characterizing molecular shape (Kier indices)
Wiener matrix: Source of novel graph invariants
Reactivity Prediction Models Applied to the Selection of Novel Candidate Building Blocks for High-Throughput Organic Synthesis of Combinatorial Libraries
Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design
Catalytic Role of Gln202 in the Carboligation Reaction Mechanism of Yeast AHAS: A QM/MM Study
Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition
The Preference Functions Method for Predicting Protein Helical Turns with Membrane Propensity
Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases
Dissociation of Membrane-Anchored Heterotrimeric G-Protein Induced by G α Subunit Binding to GTP
On the determinant of the adjacency-plus-distance matrix as the topological index for characterizing alkanes
SpeLL: An Agent for Natural Language-Driven Intelligent Spectral Modeling
Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems
MRNDR: Multihead Attention-Based Recommendation Network for Drug Repurposing
Storage and retrieval of synthetic trees
What Does the Machine Learn? Knowledge Representations of Chemical Reactivity
Structure-Based Classification of Antibacterial Activity
Molecular Orbital Functional Groups, 3. Subspectrality in the Eigenvalues of Linear Polyene Molecules and Related Aspects
Force Field Optimization using Dynamics and Ensemble Averaged Data: Vibrational Spectra and Relaxation in Bound MbCO
Three-Dimensional Quantitative Structure-Activity Relationship of Nucleosides Acting at the A 3 Adenosine Receptor: Analysis of Binding and Relative Efficacy
Modified Ant Colony Optimization Algorithm for Variable Selection in QSAR Modeling: QSAR Studies of Cyclooxygenase Inhibitors
BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript
Applications of Genetic Algorithms on the Structure-Activity Relationship Analysis of Some Cinnamamides
Getting Insights into Structural and Energetic Properties of Reciprocal Peptide-Protein Interactions
Computational Study of Dispersion and Extent of Mutated and Duplicated Sequences of the H5N1 Influenza Neuraminidase over the Period 1997-2008
Meta-Learning Enables Complex Cluster-Specific Few-Shot Binding Affinity Prediction for Protein-Protein Interactions
Cross-Target View to Feature Selection: Identification of Molecular Interaction Features in Ligand-Target Space
Design Space Exploration and Machine Learning Prediction of Hydrofluorocarbon Solubility in Ionic Liquids for Refrigerant Separation
Accurate Simulations of Water and Aqueous Solutions through Fine-Tuned Dispersion-Corrected Density Functional Theory and Machine-Learning Interatomic Potentials
The performance of a noninteractive synthesis program
AI-Augmented R-Group Exploration in Medicinal Chemistry
How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space
Computational Approaches Elucidate the Allosteric Mechanism of Human Aromatase Inhibition: A Novel Possible Route to Small-Molecule Regulation of CYP450s Activities?
Molecular Dynamics and Neural Network Analysis Reveal Sequential Gating and Allosteric Communication in FMRFamide-Activated Sodium Channels
Three-Dimensional CH/π and CH/N Interactions from Quantum-Mechanical and Database Analyses
Simulation of Organic Reactions: From the Degradation of Chemicals to Combinatorial Synthesis
Logical extension of an isomeric pseudoconversion of polycyclic aromatic hydrocarbons into acyclic polyenynes
RMechDB: A Public Database of Elementary Radical Reaction Steps
Open-Source Approach to GPU-Accelerated Substructure Search
ProPose: Steered Virtual Screening by Simultaneous Protein-Ligand Docking and Ligand-Ligand Alignment
Evaluation of neural networks based on radial basis functions and their application to the prediction of boiling points from structural parameters
Chemometrics: An Important Tool for the Modern Chemist, an Example from Wood-Processing Chemistry
Three-Dimensional Analysis of Binding Sites for Predicting Binding Affinities in Drug Design
ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields
Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies
Molecular Design Method Using a Reversible Tree Representation of Chemical Compounds and Deep Reinforcement Learning
C Programming - A Modern Approach. By K. N. King. W. W. Norton & Company: New York, 1996, 661 pp, ISBN 0-393-96945-2
Few-Shot Learning for Low-Data Drug Discovery
Mining Biological Data Using Self-Organizing Map
Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW
Cov_FB3D: A De Novo Covalent Drug Design Protocol Integrating the BA-SAMP Strategy and Machine-Learning-Based Synthetic Tractability Evaluation
Thermostability of the PYL-PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants
Fingerprint-Enhanced Graph Attention Network (FinGAT) Model for Antibiotic Discovery
Machine Learning Pipeline for Molecular Property Prediction Using ChemXploreML
Estimation of normal boiling points from group contributions
A Coarse-Grained Force Field Parameterized for MgCl 2 and CaCl 2 Aqueous Solutions
CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids
Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid
Developing a Hybrid Molecular Representation Combining Chemical Structure and MIR Spectral Data: A LogP Prediction Case Study
Fast Substructure Search in Combinatorial Library Spaces
Homology Modeling of Human Muscarinic Acetylcholine Receptors
3D QSAR Selectivity Analyses of Carbonic Anhydrase Inhibitors: Insights for the Design of Isozyme Selective Inhibitors
Stepwise Insertion of Cobra Cardiotoxin CT2 into a Lipid Bilayer Occurs as an Interplay of Protein and Membrane "Dynamic Molecular Portraits"
Challenge for Deep Learning: Protein Structure Prediction of Ligand-Induced Conformational Changes at Allosteric and Orthosteric Sites
Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations
Computer-Based Modeling in the Teaching of Steady-State Enzyme Kinetics
Comparative study of molecular descriptors derived from the distance matrix
Simulation of First-Order Chemical Kinetics Using Cellular Automata
Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning
Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures
MMSol: Predicting Protein Solubility with an Antinoise Multimodal Deep Model
MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC
Alternative Global Goodness Metrics and Sensitivity Analysis: Heuristics to Check the Robustness of Conclusions from Studies Comparing Virtual Screening Methods
Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction
QuickBooks 99
Second Indo-U.S. Workshop on Mathematical Chemistry May 30-June 3, 2000 Duluth, Minnesota
Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment
Conformational freedom in 3-D databases. 1. Techniques
VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics
A Robust Force Field Based Method for Calculating Conformational Energies of Charged Drug-Like Molecules
DrugSynthMC: An Atom-Based Generation of Drug-like Molecules with Monte Carlo Search
Parallel Computing in Computational Chemistry. Edited by Timothy G. Mattson. ACS Symposium Series 592. American Chemical Society: Washington, DC, 1995, viii + 222 pp, ISBN 0-8412-3166-4.
LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach
Modeling of Glutamate GluR6 Receptor and Its Interactions with Novel Noncompetitive Antagonists
Shaping a Screening File for Maximal Lead Discovery Efficiency and Effectiveness: Elimination of Molecular Redundancy
Charge Relaying within a Phospho-Motif Rescue Binding Competency of a Disordered Transcription Factor
Using polynomial smoothing and data bounding for the detection of nuclear material diversions and losses
PyShifts: A PyMOL Plugin for Chemical Shift-Based Analysis of Biomolecular Ensembles
Correction to "Using Predicted Bioactivity Profiles to Improve Predictive Modeling"
Modeling the Structural Basis of Human CCR5 Chemokine Receptor Function: From Homology Model Building and Molecular Dynamics Validation to Agonist and Antagonist Docking