yusuke1997/dblp-id-title huggingface dataset:
Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations
Effect of Binding on Enantioselectivity of Epoxide Hydrolase
A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins
An Efficient Method of Determining Diffusion Coefficients Using Eigenfunction Expansions
Network-Based Analysis and Characterization of Adverse Drug-Drug Interactions
NIPALSTREE: A New Hierarchical Clustering Approach for Large Compound Libraries and Its Application to Virtual Screening
Least Absolute Shrinkage and Selection Operator-Based Prediction of the Binding Constant of p -Sulfonatocalix[6]/[8]arenes with Alkaloids
An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules
BERT-AmPEP60: A BERT-Based Transfer Learning Approach to Predict the Minimum Inhibitory Concentrations of Antimicrobial Peptides for Escherichia coli and Staphylococcus aureus
Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations
Exploring Binding Sites in Chagas Disease Protein TcP21 Using Integrated Mixed Solvent Molecular Dynamics Approaches
Molecular Dynamics Simulations for Human CAR Inverse Agonists
Application of BCUT Metrics and Genetic Algorithm in Binary QSAR Analysis
Automatic assignment of molecule keywords
Problems of molecular design and the computer. 11. The FLAMINGOES program system for the nonempirical solution of structural problems of organic chemistry. The BASIC program oriented for the microcomputer
Protein Preparation Automatic Protocol for High-Throughput Inverse Virtual Screening: Accelerating the Target Identification by Computational Methods
Predicting Autoxidation of Sulfides in Drug-like Molecules Using Quantum Mechanical/Density Functional Theory Methods
autoBioSeqpy: A Deep Learning Tool for the Classification of Biological Sequences
Conformational Searching and Modeling of Transition States
Discovery of Natural Bisbenzylisoquinoline Analogs from the Library of Thai Traditional Plants as SARS-CoV-2 3CL Pro Inhibitors: In Silico Molecular Docking, Molecular Dynamics, and In Vitro Enzymatic Activity
Targeting the Receptor-Binding Motif of SARS-CoV-2 with D-Peptides Mimicking the ACE2 Binding Helix: Lessons for Inhibiting Omicron and Future Variants of Concern
QSAR Study of Ethyl 2-[(3-Methyl-2, 5-dioxo(3-pyrrolinyl))amino]-4-(trifluoromethyl) pyrimidine-5-carboxylate: An Inhibitor of AP-1 and NF-B Mediated Gene Expression Based on Support Vector Machines
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations
STAR Dictionary Definition Language: Initial Specification
MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies
The Necessity of d-Thr in the New Antibiotic Teixobactin: A Molecular Dynamics Study
CHARMM-GUI Bicelle Builder : An Extension of Membrane Builder for Modeling and Simulation of Bicelle Systems
General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor
Docking Simulation Study and Kinase Selectivity of f152A1 and Its Analogs
Relation between Distance-Based Topological Indices
Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping
A Look at the Division of Chemical Information
BGC-MAC and BGC-MAP: Attention-Based Models for Biosynthetic Gene Cluster Classification and Product Matching
Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function
A Measure of Folding Complexity for D-Dimensional Polymers
Multidimensional Drift of Sequence Attributes and Functional Profiles in the Superfamily of the Three-Finger Proteins and Their Structural Homologues
Sampling Consideration in the Selection of Fragment Screens for Chemical Substructure Search Systems
Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function
Advancing Peptide-Based Cancer Therapy with AI: In-Depth Analysis of State-of-the-Art AI Models
Optimized Data Set and Feature Construction for Substrate Prediction of Membrane Transporters
On the Misinterpretation of Our Algorithm for the Perception of Constitutional Symmetry
Mapping of Activity-Specific Fragment Pathways Isolated from Random Fragment Populations Reveals the Formation of Coherent Molecular Cores
DSX : A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes
Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification
Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning
Electronic publishing: potential benefits and problems for authors, publishers, and libraries
Chemical toxicology searching: a comparative study of online data-bases
Localized Heuristic Inverse Quantitative Structure Activity Relationship with Bulk Descriptors Using Numerical Gradients
Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation
Database of C-Glycosylporphyrins in Web Fashion
Discovery and Design of Tricyclic Scaffolds as Protein Kinase CK2 (CK2) Inhibitors through a Combination of Shape-Based Virtual Screening and Structure-Based Molecular Modification
Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1
Novel 3D Descriptors Using Excluded Volume 2: Application to Drug Classification
High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment
GlySitePred: Identification of Glycation Modification Sites Based on Deep Feature Fusion and NCR-CC Sampling Technology
Atomic Mechanisms of Transthyretin Tetramer Dissociation Studied by Molecular Dynamics Simulations
LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities
Pathway Analysis for Drug Repositioning Based on Public Database Mining
Editorial: Machine Learning in Materials Science
Beyond Woodward-Fieser Rules: Design Principles of Property-Oriented Chromophores Based on Explainable Deep Learning Optical Spectroscopy
Predicting Total Drug Clearance and Volumes of Distribution Using the Machine Learning-Mediated Multimodal Method through the Imputation of Various Nonclinical Data
GA(M)E-QSAR: A Novel, Fully Automatic Genetic-Algorithm-(Meta)-Ensembles Approach for Binary Classification in Ligand-Based Drug Design
Leveraging Bidirectional Nature of Allostery To Inhibit Protein-Protein Interactions (PPIs): A Case Study of PCSK9-LDLR Interaction
Planning of synthetic pathways on the basis of synthesis strategies
Implementation of nearest-neighbor searching in an online chemical structure search system
BalancedDiff: Balanced Diffusion Network for High-Quality Molecule Generation
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times
Platform for Unified Molecular Analysis: PUMA
Homologous G Protein-Coupled Receptors Boost the Modeling and Interpretation of Bioactivities of Ligand Molecules
Search for ABO 3 Type Ferroelectric Perovskites with Targeted Multi-Properties by Machine Learning Strategies
Binary Quantitative Structure-Activity Relationship (QSAR) Analysis of Estrogen Receptor Ligands
Stacking Interactions between 9-Methyladenine and Heterocycles Commonly Found in Pharmaceuticals
Continuous Wavelet Transform Applied to Removing the Fluctuating Background in Near-Infrared Spectra
How Do 2D Fingerprints Detect Structurally Diverse Active Compounds? Revealing Compound Subset-Specific Fingerprint Features through Systematic Selection
Chemical Databases from Springer Verlag
Automated Determination of Nuclear Magnetic Resonance Chemical Shift Perturbations in Ligand Screening Experiments: The PICASSO Web Server
Study of the Effect of Ion Channel Modulators on Photosynthetic Oxygen Evolution
Association of Two 3D QSAR Analyses. Application to the Study of Partial Agonist Serotonin-3 Ligands
LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors
On Quality Thresholds for the Clustering of Molecular Structures
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA
PharmID: Pharmacophore Identification Using Gibbs Sampling
FORTRAN Interface for Code Interoperability in Quantum Chemistry: The Q5Cost Library
Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8
ChemIntosh and ChemPanion, organic structure-drawing desk accessories for the Apple Macintosh
Using Molecular Features of Xenobiotics to Predict Hepatic Gene Expression Response
Structural and Dynamical Basis of G Protein Inhibition by YM-254890 and FR900359: An Inhibitor in Action
MCPB.py: A Python Based Metal Center Parameter Builder
Enhancing the Accuracy of Chemogenomic Models with a Three-Dimensional Binding Site Kernel
Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands
Conformation Analysis of Carotenoids in the Purple Bacterium Rhodobium marinum Based on NMR Spectroscopy and AM1 Calculation
The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening
Use of Statistical and Neural Net Approaches in Predicting Toxicity of Chemicals
Constrained Structure Minimizations on Hyperspheres for Minimum Energy Path Following
Screening of the Role of the Chemical Structure in the Electrochemical Stability Window of Ionic Liquids: DFT Calculations Combined with Data Mining
Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs
Predicting pK a by Molecular Tree Structured Fingerprints and PLS
Exploration of the Nucleation Pathway for Supramolecular Fibers
Machine Learning-Based Retention Time Prediction Tool for Routine LC-MS Data Analysis
ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn-Munkres Algorithm
Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case
Chemical Abstracts as a source for newly published books in chemistry and chemical engineering
UniMethylNet: A Universal DNA Methylation Site Prediction Network Integrating a Neural Network and an Attention Mechanism
Uncertainty Qualification for Deep Learning-Based Elementary Reaction Property Prediction
Modification and Validation of the DREIDING Force Field for Molecular Liquid Simulations (DREIDING-UT)
Structural Modeling of HCV NS3/4A Serine Protease Drug-Resistance Mutations Using End-Point Continuum Solvation and Side-Chain Flexibility Calculations
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models
Improving Covalent and Noncovalent Molecule Generation via Reinforcement Learning with Functional Fragments
Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand-Receptor Docking
A Genetic Algorithm Based on Prepotency Evolution Using Chaotic Initiation Used for Network Training
Molecular Similarity-Based Domain Applicability Metric Efficiently Identifies Out-of-Domain Compounds
Machine Learning Prediction of H Adsorption Energies on Ag Alloys
Investigation into Cyclopeptide-Based Antitumor Agents: Design, Precision Synthesis, Virtual Target Screening, and Experimental Verification
From Signal to Symphony: Exploring 2D Sequence Representations for Protein Function Prediction
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring
Thermal Sensitivity on Eccentric Gold Hollow Nanoparticles: A Perspective from Atomistic Simulations
Correction to "A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments"
Predicting the Accuracy of Ligand Overlay Methods with Random Forest Models
Computational techniques for vertex partitioning of graphs
Quantum Dynamics and Bi Metal Force Field Parameterization Yielding Significant Antileishmanial Targets
What Is the Longest Unbranched Alkane with a Linear Global Minimum Conformation?
Optimization of Cavity-Based Negative Images to Boost Docking Enrichment in Virtual Screening
Correction to Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting
Lesion Spectra: Radiation Signatures and Biological Gateways
SMINBR: An Integrated Network and Chemoinformatics Tool Specialized for Prediction of Two-Component Crystal Formation
Automatic Determination of the Sequential Order of Dynamic Data and Its Application to Vibrational Spectroscopy
Sampling and Ranking of Protein Conformations Using Machine Learning Techniques Do Not Improve the Quality of Rigid Protein-Protein Docking
Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and in Vitro Screening
Affinity Calculations of Cyclodextrin Host-Guest Complexes: Assessment of Strengths and Weaknesses of End-Point Free Energy Methods
Labeling of Benzenoid Systems which Reflects the Vertex-Distance Relations
Unraveling Disease-Associated PIWI-Interacting RNAs with a Contrastive Learning Methods
Beyond the Scope of Free-Wilson Analysis. 2 Can Distance Encoded R-Group Fingerprints Provide Interpretable Nonlinear Models?
Toward Reducing hERG Affinities for DAT Inhibitors with a Combined Machine Learning and Molecular Modeling Approach
Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a
A Novel Evaluation of Residue and Protein Volumes by Means of Laguerre Tessellation
Transfer Learning for Predicting ncRNA-Protein Interactions
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation
Immunohistochemical Analysis and Prognostic Value of Cathepsin D Determination in Laryngeal Squamous Cell Carcinoma
Development of a Chirality-Sensitive Flexibility Descriptor for 3+3D-QSAR
Self-Assembled Two-Dimensional Nanoporous Crystals as Molecular Sieves: Molecular Dynamics Studies of 1, 3, 5-Tristyrilbenzene-Cn Superstructures
Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations
Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation
Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs
Real External Predictivity of QSAR Models. Part 2. New Intercomparable Thresholds for Different Validation Criteria and the Need for Scatter Plot Inspection
A LISP program for the generation of IUPAC names from chemical structures
Insights into Ligand-Specific Activation Dynamics of Dopamine D 2 Receptor Explored by MD Simulations
Oversampling to Overcome Overfitting: Exploring the Relationship between Data Set Composition, Molecular Descriptors, and Predictive Modeling Methods
Structural similarity searching using descriptors developed for structure-activity relationship studies. [Erratum to document cited in CA117: 233063]
Coevolved Positions Represent Key Functional Properties in the Trypsin-Like Serine Proteases Protein Family
Combinatorial Preferences Affect Molecular Similarity/Diversity Calculations Using Binary Fingerprints and Tanimoto Coefficients
A Multi-Angle Approach to Predict Peptide-GPCR Complexes: The N/OFQ-NOP System as a Successful AlphaFold Application Case Study
On using graph-equivalent classes for the structure elucidation of large molecules
Chemometric Studies in the Lagoon of Venice, Italy. 1. The Environmental Quality of Water and Sediment Matrices
Irredundant Generation of Isomeric Molecular Structures with Some Known Fragments
An Efficient Lossless Compression Algorithm for Trajectories of Atom Positions and Volumetric Data
Predicting HOMO-LUMO Gaps Using Hartree-Fock Calculated Data and Machine Learning Models
CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids
CHORTLES: A Method for Representing Oligomeric and Template-Based Mixtures
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures
New method for rapid characterization of molecular shapes: applications in drug design
Toward the Comprehensive Systematic Enumeration and Synthesis of Novel Kinase Inhibitors Based on a 4-Anilinoquinazoline Binding Mode
Build-Up Algorithm for Atomic Correspondence between Chemical Structures
Semi-Empirical Born-Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package
Dynamic Workflows for Routine Materials Discovery in Surface Science
Combination of Fingerprint-Based Similarity Coefficients Using Data Fusion
Minimal Basis Set Hartree-Fock Corrected with Atom-Centered Potentials for Molecular Crystal Modeling and Crystal Structure Prediction
Human Microsomal Prostaglandin E Synthase-1 (mPGES-1) Binding with Inhibitors and the Quantitative Structure-Activity Correlation
Structural Interpretation of Activity Cliffs Revealed by Systematic Analysis of Structure-Activity Relationships in Analog Series
SWEET Family Transporters Act as Water-Conducting Carrier Proteins in Plants
Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues
Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure-Activity Relationships
Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies
Exploring Deep Learning of Quantum Chemical Properties for Absorption, Distribution, Metabolism, and Excretion Predictions
Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site
Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data
A Fast Exchange Algorithm for Designing Focused Libraries in Lead Optimization
BFMP: A Method for Discretizing and Visualizing Pyranose Conformations
Investigating Active Learning and Meta-Learning for Iterative Peptide Design
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses
Modeling the Toxicity of Chemicals to Tetrahymena pyriformis Using Heuristic Multilinear Regression and Heuristic Back-Propagation Neural Networks
Pharmacophore Screening of the Protein Data Bank for Specific Binding Site Chemistry
Recent Advances in the CLiDE Project: Logical Layout Analysis of Chemical Documents
New computer representation for chemical structures: Two-level compact connectivity tables
Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations
New Diversity Calculations Algorithms Used for Compound Selection
The Most Stable Class of Benzenoid Hydrocarbons-New Topological Correlations of Strain-Free Total Resonant Sextet Benzenoids
Shry: Application of Canonical Augmentation to the Atomic Substitution Problem
Predicting Phosphorus NMR Shifts Using Neural Networks, 2. Factors Influencing the Accuracy of Predictions
Prediction of Drug-Induced Nephrotoxicity Using Chemical Information and Transcriptomics Data
Predictive Flip Regression: A Technique for QSAR of Derivatives of Symmetric Molecules
Best of Both Worlds: Combining Pharma Data and State of the Art Modeling Technology To Improve in Silico p K a Prediction
EndNote 5 for Windows
Enhanced HTS Hit Selection via a Local Hit Rate Analysis
A Structural Isomers Enumeration and Display System (SIEDS)
Exploiting Domain Knowledge for Improved Quantitative High-Throughput Screening Curve Fitting
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA
BigSMARTS: A Topologically Aware Query Language and Substructure Search Algorithm for Polymer Chemical Structures
Estimate of Donor and Acceptor Sites Using Alternating Polarity Principle. Application to Pyridine Ring Construction
Traditional topological indexes vs electronic, geometrical, and combined molecular descriptors in QSAR/QSPR research
LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery
Bretherick's Reactive Chemical Hazards Database. Version 1.00
Compressed Binary Bit Trees: A New Data Structure For Accelerating Database Searching
ErG: 2D Pharmacophore Descriptions for Scaffold Hopping
Shape-Based Descriptors for Efficient Structure-Based Fragment Growing
Protein-Protein Binding Site Prediction by Local Structural Alignment
Protein C-GeM: A Coarse-Grained Electron Model for Fast and Accurate Protein Electrostatics Prediction
Activation and Allosteric Modulation of Human μ Opioid Receptor in Molecular Dynamics
Comparison of Multilabel and Single-Label Classification Applied to the Prediction of the Isoform Specificity of Cytochrome P450 Substrates
Exploring Multi-Scale Interaction Features through a Physics-Aware Graph Network for Enhanced Binding Affinity Prediction
Comparison of Resonance Assisted and Charge Assisted Effects in Strengthening of Hydrogen Bonds in Dipyrrins
BHB: A Simple Knowledge-Based Scoring Function to Improve the Efficiency of Database Screening
Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations
Computer-Assisted Thermal Analysis System Founded on Case-Based Reasoning
Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis
Entropic Overcompensation of the N501Y Mutation on SARS-CoV-2 S Binding to ACE2
Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids
Norton SystemWorks 2000
Binding Energy Landscape Analysis Helps to Discriminate True Hits from High-Scoring Decoys in Virtual Screening
Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis
When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values
Status of Indexing and Classification Systems and Potential Future Trends
Mechanism-Based and Computational-Driven Covalent Drug Design
Molecular Field Topology Analysis Method in QSAR Studies of Organic Compounds
Automated Protocol for Large-Scale Modeling of Gene Expression Data
Molecule Kernels: A Descriptor- and Alignment-Free Quantitative Structure-Activity Relationship Approach
PathInHydro, a Set of Machine Learning Models to Identify Unbinding Pathways of Gas Molecules in [NiFe] Hydrogenases
MHNfs: Prompting In-Context Bioactivity Predictions for Low-Data Drug Discovery
Isomerization and Decomposition of 2-Methylfuran with External Forces
Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 1. Extraction of Topological Properties
Three-Dimensional Activity Landscape Models of Different Design and Their Application to Compound Mapping and Potency Prediction
ACS Committee on Nomenclature: Annual Report for 1980
NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes
Machine Learning Assisted Clustering of Nanoparticle Structures
Canonical indexing and constructive enumeration of molecular graphs
CholMine: Determinants and Prediction of Cholesterol and Cholate Binding Across Nonhomologous Protein Structures
Identifying Biologically Active Compound Classes Using Phenotypic Screening Data and Sampling Statistics
Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory
Fast, parallel, relaxation screening for chemical patent data-base search
JChem: Java Applets and Modules Supporting Chemical Database Handling from Web Browsers