yusuke1997/dblp-id-title huggingface dataset:
Identification of Bioisosteric Substituents by a Deep Neural Network
Use of Robust Classification Techniques for the Prediction of Human Cytochrome P450 2D6 Inhibition
Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models
Discovery of Novel Selective Serotonin Reuptake Inhibitors through Development of a Protein-Based Pharmacophore
Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model
Using Graphs of Dynamic Hydrogen-Bond Networks To Dissect Conformational Coupling in a Protein Motor
Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data
Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations
Structured system of concepts for storing, retrieving, and manipulating chemical information
Algorithmically Compressed Data and the Topological Conjecture for the Inner-Core Electrons
Topological Organic Chemistry. 10. Graph Theory and Topological Indices of Conformational Isomers
RLSynC: Offline-Online Reinforcement Learning for Synthon Completion
Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches
Molecular Structure-Based Large-Scale Prediction of Chemical-Induced Gene Expression Changes
tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules
Efficient Discovery of Visible Light-Activated Azoarene Photoswitches with Long Half-Lives Using Active Search
Molecular Dynamics Simulations Reveal Structural Differences among Allelic Variants of Membrane-Anchored Cytochrome P450 2D6
DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms
Pore-Opening and Ion-Conduction Mechanism in Channelrhodopsins C1C2, ChR2, and iChloC by Computational Electrophysiology and Constant-pH Simulations
In Silico Classifiers for the Assessment of Drug Proarrhythmicity
Prediction of Ligand-Induced Structural Polymorphism of Receptor Interaction Sites Using Machine Learning
ADvisor: An Open-Source Tool for Applicability Domain Definition and Optimization in Molecular Predictive Modeling
The Production of Machine-Readable Descriptions of Chemical Reactions Using Wiswesser Line Notations
Exploring the Relationship between Nicotinic Acetylcholine Receptor Ligand Size, Efficiency, Efficacy, and C-Loop Opening
Prototype Selection Method Based on the Rivality and Reliability Indexes for the Improvement of the Classification Models and External Predictions
What is in a patent? Information: but can I find it?
Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure-Activity Resource 2013 and 2014 Blind Challenges
ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 4. Chemical Reactions
LLM-Driven Synthesis Planning for Quantum Dot Materials Development
ACD/Spectrus Processor Review
A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application
Mining Statistically Significant Molecular Substructures for Efficient Molecular Classification
Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis
Accuracy Assessment of Protein-Based Docking Programs against RNA Targets
Modeling and Elucidating the Behavior of a Thermoresponsive LCST Ionic Liquid
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces
Ligand Bias of Scoring Functions in Structure-Based Virtual Screening
Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions
Disentangling Folding from Energetic Traps in Simulations of Disordered Proteins
Structure-Activity Study on Antiulcer Agents Using Wiener's Topological Index and Molecular Connectivity Index
Orthogonalization of Block Variables by Subspace-Projection for Quantitative Structure Property Relationship (QSPR) Research
MolProphet: A One-Stop, General Purpose, and AI-Based Platform for the Early Stages of Drug Discovery
Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion
ROSHAMBO2: Accelerating Molecular Alignment for Large Chemical Libraries with GPU Optimization and Algorithmic Advances
Simulation of Interface Characteristics and Charge Transfer Dynamics for Layered Electrodes Using Cascade Capacitance in Supercapacitors by COMSOL Software
Automated Calibration of a Poly(oxymethylene) Dimethyl Ether Oxidation Mechanism Using the Knowledge Graph Technology
Exhaustive DFTB Parameterization and Its Implementation for the Exploration of Ag Nanostructures + H 2 O Complexes
GA Strategy for Variable Selection in QSAR Studies: Application of GA-Based Region Selection to a 3D-QSAR Study of Acetylcholinesterase Inhibitors
Molecular Quantum Similarity Matrix Based Clustering of Molecules Using Dendrograms
Correction to "A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery"
LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations
Superposition of Three-Dimensional Chemical Structures Allowing for Conformational Flexibility by a Hybrid Method
A Machine Learning Approach for Predicting HIV Reverse Transcriptase Mutation Susceptibility of Biologically Active Compounds
Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening
A Machine-Learned "Chemical Intuition" to Overcome Spectroscopic Data Scarcity
iLOGP: A Simple, Robust, and Efficient Description of n -Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach
Improved Docking of Polypeptides with Glide
Large-Scale Distributed Training of Transformers for Chemical Fingerprinting
A Searchable Database for Comparing Protein-Ligand Binding Sites for the Analysis of Structure-Function Relationships
WIN55212-2 Docking to the CB 1 Cannabinoid Receptor and Multiple Pathways for Conformational Induction
Evolutionary-Algorithm-Based Strategy for Computer-Assisted Structure Elucidation
First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach
Combining Global and Local Measures for Structure-Based Druggability Predictions
Nonproductive Binding Modes as a Prominent Feature of Aβ40 Fiber Elongation: Insights from Molecular Dynamics Simulation
Two programs to further popular literacy in technology
Enhancing Molecular Representations Via Graph Transformation Layers
Irreducible tensor bases for the Frobenius algebra of a finite unitary group
Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors
STable AutoCorrelation Integral Estimator: Robust and Accurate Transport Properties from Molecular Dynamics Simulations
Using Novel Descriptor Accounting for Ligand-Receptor Interactions To Define and Visually Explore Biologically Relevant Chemical Space
Molecular Dynamics of Fibrinogen Adsorption onto Graphene, but Not onto Poly(ethylene glycol) Surface, Increases Exposure of Recognition Sites That Trigger Immune Response
Understanding Interactions of Curcumin with Lipid Bilayers: A Coarse-Grained Molecular Dynamics Study
Tandem Allosteric Effects of Reactant and Product that Promote Deacetylation Cycles in Sir2
GMA: A Generic Match Algorithm for Structural Homomorphism, Isomorphism, and Maximal Common Substructure Match and Its Applications
RISC: Rapid Inverted-Index Based Search of Chemical Fingerprints
Chemical-Space-Based de Novo Design Method To Generate Drug-Like Molecules
Automatic interpretation of the texts of chemical patent abstracts. 2. Processing and results
Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions
Design of New Plasmepsin Inhibitors: A Virtual High Throughput Screening Approach on the EGEE Grid
Heterogeneous Graph Contrastive Learning with Graph Diffusion for Drug Repositioning
Applications and Advances in Machine Learning Force Fields
Discrimination and Molecular Design of New Theoretical Hypolipaemic Agents Using the Molecular Connectivity Functions
Automated Extraction of Information on Chemical-P-glycoprotein Interactions from the Literature
Evaluating Computational Chemistry Methods for Isotopic Fractionation between CO2(g) and H2O(g)
Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities
A Topological Account of Chirality
Smart Reaction Templating: A Graph-Based Method for Automated Molecular Dynamics Input Generation
AlvaBuilder: A Software for De Novo Molecular Design
Water Networks in Complexes between Proteins and FDA-Approved Drugs
Molecular Similarity. 1. Analytical Description of the Set of Graph Similarity Measures
Augmentation of MS/MS Libraries with Spectral Interpolation for Improved Identification
Extended Template-Based Modeling and Evaluation Method Using Consensus of Binding Mode of GPCRs for Virtual Screening
Functional Ceramic Materials Database: An Online Resource for Materials Research
G-Protein Coupled Receptors Virtual Screening Using Genetic Algorithm Focused Chemical Space
The Information Content of Titles in Contraception Literature
Dynamics of Noncovalent Interactions in All-α and All-β Class Proteins: Implications for the Stability of Amyloid Aggregates
Constructing Protein Models for Ligand-Receptor Binding Thermodynamic Simulations: An Application to a Set of Peptidometic Renin Inhibitors
Ligand-Protein Cross-Docking with Water Molecules
Development of R-Group Fingerprints Based on the Local Landscape from an Attachment Point of a Molecular Structure
Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting
Bridging and Interlinking the Information Resources
Molecules in Silico: A Graph Description of Chemical Reactions
Conservation and Relevance of Pharmacophore Point Types
Correction to Citation in "Combined In Vitro and In Silico Workflow to Deliver Robust, Transparent, and Contextually Rigorous Models of Bioactivity"
Microelectronics in analytical chemistry
Clustering Peptide Structures through Identification of Commonly Exposed Groups
Assessing the Discriminatory Power of Scoring Functions for Virtual Screening
Comparison of Molecular Fingerprint Methods on the Basis of Biological Profile Data
Computational Polypharmacology Analysis of the Heat Shock Protein 90 Interactome
Lin_F9: A Linear Empirical Scoring Function for Protein-Ligand Docking
GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD
REPROVIS-DB: A Benchmark System for Ligand-Based Virtual Screening Derived from Reproducible Prospective Applications
Anatomy of High-Performance 2D Similarity Calculations
Computer-Aided Spectral Indentification of Laser-Induced Plasma Emission
Review of Lotus 123 Release 4 for Windows
P4ward: An Automated Modeling Platform for Protac Ternary Complexes
Targeting the Conformational Transitions of MDM2 and MDMX: Insights into Dissimilarities and Similarities of p53 Recognition
GraphPad Prism, Data Analysis, and Scientific Graphing
How To Find Chemical Information: A Guide for Practicing Chemists, Educators, and Students 3rd ed.; By Robert E. Maizell. John Wiley & Sons, Inc.: New York, 1998, 515 pp, ISBN 0471125792
New Combined Model for the Prediction of Regioselectivity in Cytochrome P450/3A4 Mediated Metabolism
Different Binding Modes of Structurally Diverse Ligands for Human D3DAR
Join Persistent Homology (JPH)-Based Machine Learning for Metalloprotein-Ligand Binding Affinity Prediction
ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 5. Experiment Planning and Product Design
TransABseq: A Two-Stage Approach for Predicting Antigen-Antibody Binding Affinity Changes upon Mutation Based on Protein Sequences
PLUMS: a Program for the Rapid Optimization of Focused Libraries
Chemical and spectral databases: a look into the future
COSMO sar3D : Molecular Field Analysis Based on Local COSMO σ-Profiles
Computational Studies of Bacterial Resistance to β-Lactam Antibiotics: Mechanism of Covalent Inhibition of the Penicillin-Binding Protein 2a (PBP2a)
Molecular Dynamics and Machine Learning Study of Adrenaline Dynamics in the Binding Pocket of GPCR
Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution
MultiDK: A Multiple Descriptor Multiple Kernel Approach for Molecular Discovery and Its Application to Organic Flow Battery Electrolytes
Computer Assisted Simulation of 13C Nuclear Magnetic Spectra of Monosaccharides
MolBook UNIPI─Create, Manage, Analyze, and Share Your Chemical Data for Free
BartSmiles: Generative Masked Language Models for Molecular Representations
Similarity Searching Using Reduced Graphs
Peripheral Linker Mediates Acyl Carrier Protein's Recognition of Dehydratase and Stabilizes Type-I Mycobacterium tuberculosis Fatty Acid Synthase
Data Mining the NCI Cancer Cell Line Compound GI 50 Values: Identifying Quinone Subtypes Effective Against Melanoma and Leukemia Cell Classes
Modeling Studies of Binding of Sea Raven Type II Antifreeze Protein to Ice
Predicting Key Example Compounds in Competitors' Patent Applications Using Structural Information Alone
A Selectivity Study of FFAR4/FFAR1 Agonists by Molecular Modeling
ACS Committee on Nomenclature: Annual Report for 1987
From Chemical Topology to 3D Geometry
Cheminformatics Modeling of Adverse Drug Responses by Clinically Relevant Mutants of Human Androgen Receptor
Revealing New Insights into the Dynamics of Human Aromatase Interacting with Cytochrome P450 Reductase in a Realistic Membrane Environment
Dynamics Playing a Key Role in the Covalent Binding of Inhibitors to Focal Adhesion Kinase
Mini-fingerprints Detect Similar Activity of Receptor Ligands Previously Recognized Only by Three-Dimensional Pharmacophore-Based Methods
Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation
Demystifying Multitask Deep Neural Networks for Quantitative Structure-Activity Relationships
Luciferase Advisor: High-Accuracy Model To Flag False Positive Hits in Luciferase HTS Assays
Modeling Chemical Reaction Networks Using Neural Ordinary Differential Equations
Assessing Different Classification Methods for Virtual Screening
Statistical Analysis, Investigation, and Prediction of the Water Positions in the Binding Sites of Proteins
Molecular Dynamics Simulations of Reduced and Oxidized TFIIIA Zinc Fingers Free and Interacting with 5S RNA
Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations
Mapping Algorithms for Molecular Similarity Analysis and Ligand-Based Virtual Screening: Design of DynaMAD and Comparison with MAD and DMC
Computational chemistry network services and user interfacing
AI Promoted Virtual Screening, Structure-Based Hit Optimization, and Synthesis of Novel COVID-19 S-RBD Domain Inhibitors
MolPipeline: A Python Package for Processing Molecules with RDKit in Scikit-learn
Ensemble Docking for Intrinsically Disordered Proteins
Pan-Cancer Analysis of G Protein-Coupled Receptors as Cancer Driver Genes and Drug Repurposing Targets
A View on Molecular Complexity from the GDB Chemical Space
Modification of the Wiener Index. 2
Exploring Structure-Sensitive Relations for Small Species Adsorption Using Machine Learning
Preventing AI From Creating Biochemical Threats
TCnet: A Novel Strategy to Predict Target Combination of Alzheimer's Disease via Network-Based Methods
TeroKit: A Database-Driven Web Server for Terpenome Research
HPTRMF: Collaborative Matrix Factorization-Based Prediction Method for LncRNA-Disease Associations Using High-Order Perturbation and Flexible Trifactor Regularization
Entropic Trapping Binding Mechanism: Its Likely Role in Receptor-Ligand and Other Biochemical Systems
Automatized Assessment of Protective Group Reactivity: A Step Toward Big Reaction Data Analysis
Classifier Ensemble Based on Feature Selection and Diversity Measures for Predicting the Affinity of A 2B Adenosine Receptor Antagonists
Modeling of Nontraditional Structures of Carbon
Use of Pruned Computational Neural Networks for Processing the Response of Oscillating Chemical Reactions with a View to Analyzing Nonlinear Multicomponent Mixtures
MF-PCBA: Multifidelity High-Throughput Screening Benchmarks for Drug Discovery and Machine Learning
Exploring Peptide-likeness of Active Molecules Using 2D Fingerprint Methods
TRIM21-Driven Degradation of BRD4: Development of Heterobifunctional Degraders and Investigation of Recruitment and Selectivity Mechanisms
Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid
Distinct Molecular Surfaces and Hydrophobicity of Amino Acid Residues in Proteins
CRAACK: Consensus Program for NMR Amino Acid Type Assignment
Variable Connectivity Index for Cycle-Containing Structures
Interpreting Computational Neural Network Quantitative Structure-Activity Relationship Models: A Detailed Interpretation of the Weights and Biases
Benchmarking of Model Core Potentials: Application to the Halogen Complexes of Group 4 Metals
Bounds for the Randi Connectivity Index
Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions
General formulas for the Wiener Index
Correction to "Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers"
GPCR-BERT: Interpreting Sequential Design of G Protein-Coupled Receptors Using Protein Language Models
Deciphering a Pharmacophore Network: A Case Study Using BCR-ABL Data
Combined Computational and Structural Approach into Understanding the Role of Peptide Binding and Activation of Melanocortin Receptor 4
Comparison of Three Preprocessing Filters Efficiency in Virtual Screening: Identification of New Putative LXRβ Regulators As a Test Case
WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures
Editorial: Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery
Automated Additive Modeling Techniques Applied to Thermochemical Property Estimation
Integrated Decision Support for Assessing Chemical Liabilities
Coordinate-Free and Low-Order Scaling Machine Learning Model for Atomic Partial Charge Prediction for Any Size of Molecules
Understanding the Catalytic Mechanism and the Substrate Specificity of an Engineered Gluten Hydrolase by QM/MM Molecular Dynamics and Free Energy Simulations
Molecular Dynamics Integration Meets Standard Theory of Molecular Vibrations
Effects of Mutating Trp42 Residue on γD-Crystallin Stability
Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes
Computational Techniques for the Automorphism Groups of Graphs
Explainable Analysis for New Psychoactive Substance Identification with Chemical Insights
Analysis of the Relationship among the Graphs Isomorphic to Multilayered Cyclic Fence Graphs (MLCFG)
Short Nonbonded Contact Distances in Organic Molecules and Their Use as Atom-Clash Criteria in Conformer Validation and Searching
Recent Advances in PC-Linux Systems for Electronic Structure Computations by Optimized Compilers and Numerical Libraries
On the Stability of CoMFA Models
Conformational Dynamics of thiM Riboswitch To Understand the Gene Regulation Mechanism Using Markov State Modeling and the Residual Fluctuation Network Approach
Virtual Screening Yields Inhibitors of Novel Antifungal Drug Target, Benzoate 4-Monooxygenase
Optimized Partition of Minimum Spanning Tree for Piecewise Modeling by Particle Swarm Algorithm. QSAR Studies of Antagonism of Angiotensin II Antagonists
Data Structure Comparison Using Box Counting Analysis
Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes
Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns
Mechanism of Cytochrome P450 17A1-Catalyzed Hydroxylase and Lyase Reactions
Evaluation of a 1H-13C NMR Spectral Library
Impact of Glycans Modulating Human Cytomegalovirus Glycoprotein B on Broad-Spectrum Neutralizing Human Antibody Recognition: Unveiled by Molecular Dynamics Simulation
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison
Searching Chemical Abstracts vs. CA Condensates
Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions
Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds
GPCR-Tailored Pharmacophore Pattern Recognition of Small Molecular Ligands
Pharmacoprint: A Combination of a Pharmacophore Fingerprint and Artificial Intelligence as a Tool for Computer-Aided Drug Design
Instigating the In Vitro Anticancer Activity of New Pyridine-Thiazole-Based Co(III), Mn(II), and Ni(II) Complexes: Synthesis, Structure, DFT, Docking, and MD Simulation Studies
Different Zeroes of Interaction Energies As the Cause of Opposite Results on the Stabilizing Nature of C-H···O Intramolecular Interactions
Time-Domain Analysis of Molecular Dynamics Trajectories Using Deep Neural Networks: Application to Activity Ranking of Tankyrase Inhibitors
QSAR-Co: An Open Source Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models
Expert Systems and Analytical Chemistry: Recent Progress in the ACexpert Project
An expert system for analytical data management
Molecular Dynamics Study to Investigate the Dimeric Structure of the Full-Length α-Synuclein in Aqueous Solution
Conformational Changes of Thyroid Receptors in Response to Antagonists
High-Throughput Screening and Prediction of Nucleophilicity of Amines Using Machine Learning and DFT Calculations
Computation of Induced Dipoles in Molecular Mechanics Simulations Using Graphics Processors
Applications of Mathematics to Structural Chemistry
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD
Extending the Martini Coarse-Grained Force Field to N-Glycans
Information System, Data Bases, and On-Line Services of the Japan Information Center of Science and Technology (JICST)
The Fuzzy Hierarchical Cross-Clustering Algorithm. Improvements and Comparative Study
FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method
Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation
Mechanism of Glycans Modulating Cholesteryl Ester Transfer Protein: Unveiled by Molecular Dynamics Simulation
A General QSPR Treatment for Dielectric Constants of Organic Compounds
Nonadditive Interactions in Trimers Containing H2, N2, and O2
An interpretation of Chemical Abstracts Service indexing policies
Physiognomy of numeric/factual chemical and material property data
Rational Design of Novel Glycomimetic Peptides for E-Selectin Targeting
Toward Generating Simpler QSAR Models: Nonlinear Multivariate Regression versus Several Neural Network Ensembles and Some Related Methods
Carbohydrate Structure Generalization Scheme for Database-Driven Simulation of Experimental Observables, Such as NMR Chemical Shifts
Ab Initio Stochastic Optimization of Conformational and Many-Body Degrees of Freedom
Application of Transformers in Cheminformatics
How Does the Methodology of 3D Structure Preparation Influence the Quality of p K a Prediction?
Structural Distortion of β-Cyclodextrin Plays a Key Role in the pH-dependent Host-Guest Chemistry with Doxorubicin, Evident by the Electrochemical and Molecular Dynamics Approach
3D QSAR Studies on Protein Tyrosine Phosphatase 1B Inhibitors: Comparison of the Quality and Predictivity among 3D QSAR Models Obtained from Different Conformer-Based Alignments
Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses