yusuke1997/dblp-id-title huggingface dataset:
Additive and Nonadditive Effects of Two Factors on a Response Function
COLOR: A Compositional Linear Operation-Based Representation of Protein Sequences for Identification of Monomer Contributions to Properties
Locating Large, Flexible Ligands on Proteins
Toward Multiscale Modeling of Proteins and Bioagglomerates: An Orientation-Sensitive Diffusion Model for the Integration of Molecular Dynamics and the Discrete Element Method
Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials
Quantitative Polypharmacology Profiling Based on a Multifingerprint Similarity Predictive Approach
Atomic Chirality, a Quantitative Measure of the Chirality of the Environment of an Atom
Ligand-Based Virtual Screening Approach Using a New Scoring Function
Production of a Hierarchical Chemical Thesaurus
Diversity and Chemical Library Networks of Large Data Sets
Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands
A User's Experience with the Derwent Patent Files
Three-Dimensional Quantitative Structure-Activity Relationship (QSAR) and Receptor Mapping of Cytochrome P-45014DM Inhibiting Azole Antifungal Agents1
Pattern and Dynamics of FLT3 Duplications
How Experimental Errors Influence Drug Metabolism and Pharmacokinetic QSAR/QSPR Models
Investigating the Dynamics of the KCNN4 Channel: From the Determination of the Complete K + Permeation Pathway Across the Channel to Its Opening by PIP2
Kernel Target Alignment Parameter: A New Modelability Measure for Regression Tasks
CACPP: A Contrastive Learning-Based Siamese Network to Identify Anticancer Peptides Based on Sequence Only
Translocation Mechanism of Allosteric Sodium Ions in β 2 -Adrenoceptor
CoMFA, CoMSIA, and Molecular Hologram QSAR Studies of Novel Neuronal nAChRs Ligands-Open Ring Analogues of 3-Pyridyl Ether
The Valence Overall Wiener Index for Unsaturated Hydrocarbons
RUBIDIUM, a program for computer-aided assignment of two-dimensional NMR spectra of polypeptides
MIMUMBA Revisited: Torsion Angle Rules for Conformer Generation Derived from X-ray Structures
Novel Method for Pharmacophore Analysis by Examining the Joint Pharmacophore Space
Impact of Conformational Flexibility on Three-Dimensional Similarity Searching Using Correlation Vectors
Prediction and Optimization of NaV1.7 Sodium Channel Inhibitors Based on Machine Learning and Simulated Annealing
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design
Predictivity of QSAR
De Novo Peptide and Protein Design Using Generative Adversarial Networks: An Update
StackPIP: An Effective Computational Framework for Accurate and Balanced Identification of Proinflammatory Peptides
New Quantum Mechanics-Based Three-Dimensional Molecular Descriptors for Use in QSSR Approaches: Application to Asymmetric Catalysis
Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study
Similarity Search Profiling Reveals Effects of Fingerprint Scaling in Virtual Screening
Molecular Mechanism underlying PRMT1 Dimerization for SAM Binding and Methylase Activity
Similarity-Potency Trees: A Method to Search for SAR Information in Compound Data Sets and Derive SAR Rules
A Hybrid Approach to Structure and Function Modeling of G Protein-Coupled Receptors
Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics
A Neural Device for Searching Direct Correlations between Structures and Properties of Chemical Compounds
Receptor-Based Modeling and 3D-QSAR for a Quantitative Production of the Butyrylcholinesterase Inhibitors Based on Genetic Algorithm
De Novo Design of Cyclic Peptide Binders Based on Fragment Docking and Assembling
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein
Tension Enhances the Binding Affinity of β1 Integrin by Clamping Talin Tightly: An Insight from Steered Molecular Dynamics Simulations
Homology Models of Human All-Trans Retinoic Acid Metabolizing Enzymes CYP26B1 and CYP26B1 Spliced Variant
Construction of a Virtual High Throughput Screen by 4D-QSAR Analysis: Application to a Combinatorial Library of Glucose Inhibitors of Glycogen Phosphorylase b
End-user searching: the Amoco experience
Sequential assignment of 2D-NMR spectra of proteins using genetic algorithms
PyPEF - An Integrated Framework for Data-Driven Protein Engineering
Polarizabilities of Solvents from the Chemical Composition
Structural Insights into the Cofactor Role of Heparin/Heparan Sulfate in Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II
Interpretation of Kuratowski's theorem in graph theory as both a topological abstraction and a chemical reality
Enhancing Retrosynthetic Reaction Prediction with Deep Learning Using Multiscale Reaction Classification
Nanomaterial Synthesis Insights from Machine Learning of Scientific Articles by Extracting, Structuring, and Visualizing Knowledge
Strategy To Discover Diverse Optimal Molecules in the Small Molecule Universe
Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa
Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach
Adobe After Effects 7.0 - Studio Techniques By Mark Christiansen. Adobe (Peachpit) Press: Berkeley, CA, 2006, 576 pp and DVD. ISBN 0-321-38552-7. Softcover. U.S. $54.99
Benefit of Retraining p K a Models Studied Using Internally Measured Data
The Wiener Index and the Szeged Index of Benzenoid Systems in Linear Time
NIH/EPA Chemical Information System
Computing a New Family of Shape Descriptors for Protein Structures
Fluorine Bonding - How Does It Work In Protein-Ligand Interactions?
MuLiMs-MCoMPAs: A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors
Conformational Analysis of the Loop-to-Helix Transition of the α-Helix3 Plastic Region in the N-Terminal Domain of Human Hsp90α by a Computational Biochemistry Approach
Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery
Linear Free Energy Relationship Correlation of the Distribution of Solutes between Water and Sodium Dodecyl Sulfate (SDS) Micelles and between Gas and SDS Micelles
Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using in Silico Screening
Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations
Inhibitors of PIM-1 Kinase: A Computational Analysis of the Binding Free Energies of a Range of Imidazo [1, 2-b] Pyridazines
Szeged Index of Symmetric Graphs
Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures
Correction to "Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis"
Correction to "Interaction Patterns of Pyrazolopyrimidines with Receptor Proteins"
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C
Copyright Impacts of and on Government Programs
Enrichment Analysis for Discovering Biological Associations in Phenotypic Screens
Automatic extraction of ring substructures from a chemical structure
Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites
Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches
Enumeration, Generation, and Construction of Stereoisomers of High-Valence Stereocenters
Comparative Study on the Use of Docking and Bayesian Categorization To Predict Ligand Binding to Nicotinic Acetylcholine Receptors (nAChRs) Subtypes
EFGs: A Complete and Accurate Implementation of Ertl's Functional Group Detection Algorithm in RDKit
Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis
StrukEd-The Structural Chemistry Interface
Expanding the Range of Force Fields Available for ONIOM Calculations: The SICTWO Interface
Computer-Aided Molecular Design. Theory and Practice. By Jean-Pierre Doucet and Jacques Weber. Academic Press: San Diego, 1996, 457 pp, ISBN 0-12-221285-1
QSAR Models for the Prediction of Binding Affinities to Human Serum Albumin Using the Heuristic Method and a Support Vector Machine
External Electric Field Effects on AFM-like Magnetism in Nitroxide-Functionalized C + :C Base Pair
Structural and Thermodynamic Insights into Competitive Binding of the EGR1 and Sp1 Zinc Finger Class of Transcription Factors with a GC-Rich DNA Motif
Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients
He Inclusion in Ice-like and Clathrate-like Frameworks: A Benchmark Quantum Chemistry Study of Guest-Host Interactions
Serverless Prediction of Peptide Properties with Recurrent Neural Networks
Searching the "Biologically Relevant"Conformation of Dopamine: A Computational Approach
Modeling Toxicity by Using Supervised Kohonen Neural Networks
Computer Aided Olive Oil-Gas Partition Coefficient Calculations
Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex
WordPerfect 9
Disjoint Molecular Orbitals in Nonalternant Conjugated Diradical Hydrocarbons
Characterization of Hydration Properties in Structural Ensembles of Biomolecules
Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations
Dedenser: A Python Package for Clustering and Downsampling Chemical Libraries
Identification of Macrophage-Associated Novel Drug Targets in Atherosclerosis Based on Integrated Transcriptome Features
Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity
Alignment-Based Prediction of Sites of Metabolism
Kernel Density Estimation Applied to Bond Length, Bond Angle, and Torsion Angle Distributions
Introduction of Jumping Fragments in Combination with QSARs for the Assessment of Classification in Ecotoxicology
Computer-Aided Molecular Design of Asymmetric Pyrazole Derivatives with Exceptional Enantioselective Recognition toward the Chiralcel OJ-H Stationary Phase
Object-oriented programming applied to laboratory automation. 1. An icon-based user interface for the Analytical Director
Dual-Site Targeting by Peptide Inhibitors of the N-Terminal Domain of Hsp90: Mechanism and Design
Density Functional Theory Study on the Formation of Reactive Benzoquinone Imines by Hydrogen Abstraction
Beyond the Ground State: Predicting Electron Ionization Mass Spectra Using Excited-State Molecular Dynamics
Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4
SpecInfo: An integrated spectroscopic information system
Neural Networks: Accurate Nonlinear QSAR Model for HEPT Derivatives
Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14
Women in Computational Chemistry
Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation
Similarity searching in databases of three-dimensional molecules and macromolecules
DrugLogit: Logistic Discrimination between Drugs and Nondrugs Including Disease-Specificity by Assigning Probabilities Based on Molecular Properties
Review of Pro-Cite 3 for Windows
Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy
Organic Synthesis - Art or Science?
Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid-Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain
Discovery of FDA-Approved Drugs as Inhibitors of Fatty Acid Binding Protein 4 Using Molecular Docking Screening
A simple method for the representation, quantification, and comparison of the volumes and shapes of chemical compounds
Subangstrom Accuracy in pHLA-I Modeling by Rosetta FlexPepDock Refinement Protocol
Patent Information Needs from a Marketing Manager's Point of View
Improving the Performance of MM/PBSA in Protein-Protein Interactions via the Screening Electrostatic Energy
Knowledge representation using an augmented planning network: application to an expert system for planning HPLC separations
Insolubility Classification with Accurate Prediction Probabilities Using a MetaClassifier
Order Theoretical Tools for the Evaluation of Complex Regional Pollution Patterns
APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries
Comparison between Neural Networks (NN) and Principal Component Analysis (PCA): Structure Activity Relationships of 1, 4-Dihydropyridine Calcium Channel Antagonists (Nifedipine Analogues)
Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold
Quantum Mechanics-Based Properties for 3D-QSAR
MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands
QSPR Modeling for Solubility of Fullerene (C60) in Organic Solvents
Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations
A Unified Deep Graph Model for Identifying the Molecular Categories of Ligands Targeting Nuclear Receptors
Multimodal Feature Fusion for Bone Toxicity Prediction and Local Platform
Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2
Requirements for and challenges associated with submission of machine-readable manuscripts
Errata-Computer-Based Modeling in the Teaching of Steady-State Enzyme Kinetics
Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter
Morphology of a Transmembrane Aβ 42 Tetramer via REMD Simulations
Identification of Toxifying and Detoxifying Moieties for Mutagenicity Prediction by Priority Assessment
Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density
SARANEA: A Freely Available Program To Mine Structure-Activity and Structure-Selectivity Relationship Information in Compound Data Sets
MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing
Evaluation of Computational Chemistry Methods: Crystallographic and Cheminformatics Analysis of Aminothiazole Methoximes
Generating and counting unbranched catacondensed benzenoids
Predicting the Minimal Inhibitory Concentration for Antimicrobial Peptides with Rana-Box Domain
A new algorithm for selection of synthetically important rings. The essential set of essential rings for organic structures
On the Relation between Retention Indexes and the Interaction between the Solute and the Column in Gas-Liquid Chromatography
Patent Symposium Papers
The Vibrational Spectra of the Boron Halides and Their Molecular Complexes, 3. Ab Initio Predictions of the Structures, Energetics, and Mulliken Atomic Charges of the Complexes of Boron Trifluoride with Some Linear Nitrogen Donors
Analysis of Progress Curves in an Acetylcholinesterase Reaction: A Numerical Integration Treatment
Multiple constructions in synthesis design
THERM: a computer code for estimating thermodynamic properties for species important to combustion and reaction modeling
Degeneracy of Topologic Distance Descriptors for Cubic Molecular Graphs: Examples of Small Fullerenes
Exploration and Evaluation of Machine Learning-Based Models for Predicting Enzymatic Reactions
Discovery of Novel 5-Lipoxygenase-Activating Protein (FLAP) Inhibitors by Exploiting a Multistep Virtual Screening Protocol
Hybrid Genetic Algorithm with an Adaptive Penalty Function for Fitting Multimodal Experimental Data: Application to Exchange-Coupled Non-Kramers Binuclear Iron Active Sites
Applications of Ensemble Docking in Potential Inhibitor Screening forMycobacterium tuberculosisIsocitrate Lyase Using a Local Plant Database
Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE
Merging Applicability Domains for in Silico Assessment of Chemical Mutagenicity
An Effective Virtual Screening Protocol To Identify Promising p53-MDM2 Inhibitors
RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks
HyperNMR for Windows
Similarity searching in files of three-dimensional chemical structures. Implementation of atom mapping on the distributed array processor DAP-610, the MasPar MP-1104, and the connection machine CM-200
Exhaustive Generation of Organic Isomers, 4. Acyclic Stereoisomers with One or More Chiral Carbon Atoms
Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches
Parallel and Antiparallel β-Strands Differ in Amino Acid Composition and Availability of Short Constituent Sequences
A comment on nomenclature and the unsaturated bond
The Merck Index Twelfth Edition on CD-ROM Version 12: 1 1996 for Microsoft Windows1
S N Ar Regioselectivity Predictions: Machine Learning Triggering DFT Reaction Modeling through Statistical Threshold
Enhanced Regioselectivity Prediction of sp 2 C-H Halogenation via Negative Data Augmentation and Multimodel Integration
Computer Coding of Configuration
Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions
TargetTox: A Feature Selection Pipeline for Identifying Predictive Targets Associated with Drug Toxicity
Conformational Selectivity of ITK Inhibitors: Insights from Molecular Dynamics Simulations
PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins
Substructure searching of heterocycles by computer generation of potential aliphatic precursor
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering
Graphical Representation for Automated Retrieval of a Class of Fused Six-Rings
Inhibitors of SARS-3CL pro : Virtual Screening, Biological Evaluation, and Molecular Dynamics Simulation Studies
Structure-Activity Relationship and Comparative Docking Studies for Cycloguanil Analogs as PfDHFR-TS Inhibitors
A Scalable and Generalizable Method to Minimize Solvent Interference in Identification of Chemical Reaction Networks from Spectroscopic Data
Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design
In Silico Footprinting of Ligands Binding to the Minor Groove of DNA
Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves
Reduced Dimensional Representations of Molecular Structure
Systematic Signatures for Organic Reactions
PREFER: A New Predictive Modeling Framework for Molecular Discovery
Overcoming Small Data Limitations in Materials Informatics: Interpretable Predictive Modeling of Optical Limiting Efficiency Using the CORRELATO Algorithm
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites
Design of Highly Potent Antibiofilm, Antimicrobial Peptides Using Explainable Artificial Intelligence
Substructure Retrieval by Means of the BASIC Fragment Search Dictionary Based on the Chemical Abstracts Service Chemical Registry III System
Ranking Using the Copeland Score: A Comparison with the Hasse Diagram
Control of Synthetic Feasibility of Compounds Generated with CReM
Basis for Accurate Protein p K a Prediction with Machine Learning
Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations
PMODiff: Physics-Informed Multi-Objective Optimization Diffusion Model for Protein-Specific 3D Molecule Generation
Insights into Selectin Inhibitor Design from Endogenous Isomeric Ligands of SLea and SLex
Virtual Screening Data Fusion Using Both Structure- and Ligand-Based Methods
Expert-Guided Substructure Information Bottleneck for Molecular Property Prediction
Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes
How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency
MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams
Classification of Environmental Estrogens by Physicochemical Properties Using Principal Component Analysis and Hierarchical Cluster Analysis
Data Compression of Large Document Data Bases
Structure-Based Classification of Chemical Reactions without Assignment of Reaction Centers
A New Approach to Radial Basis Function Approximation and Its Application to QSAR
A Structure-Activity Study of Taxol, Taxotere, and Derivatives Using the Electronic Indices Methodology (EIM)
Mechanistic Insights into the Nonenzymatic Biosynthesis of Artemisinin and Related Natural Products: A Quantum Chemical Study
CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction
Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase-Ligand Interactions
What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling
Hydrophobic Ligand Entry and Exit Pathways of the CB1 Cannabinoid Receptor
Bioturbo Similarity Searching: Combining Chemical and Biological Similarity To Discover Structurally Diverse Bioactive Molecules
Combined MEDV-GA-MLR Method for QSAR of Three Panels of Steroids, Dipeptides, and COX-2 Inhibitors
Comparison of Beilstein CrossFirePlusReactions and the Selective Reaction Databases under ISIS
PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges
Drug-like Annotation and Duplicate Analysis of a 23-Supplier Chemical Database Totalling 2.7 Million Compounds
Chemical Descriptors for a Large-Scale Study on Drop-Weight Impact Sensitivity of High Explosives
Comprehensive Structural and Thermodynamic Analysis of Prefibrillar WT α-Synuclein and Its G51D, E46K, and A53T Mutants by a Combination of Small-Angle X-ray Scattering and Variational Bayesian Weighting
HADDOCK 2P2I : A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors
Prediction of Blood-Βrain Partitioning and Human Serum Albumin Binding Based on COSMO-RS σ-Moments
PROSIT: Pseudo-Rotational Online Service and Interactive Tool, Applied to a Conformational Survey of Nucleosides and Nucleotides
On the Difficulty to Rescore Hits from Ultralarge Docking Screens
Similarity in organic chemistry: A summary of the Beilstein Institute Conference
Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models
Simple Construction of Embedding Frequencies of Trees and Rooted Trees
Comparative Assessment of Scoring Functions: The CASF-2016 Update
Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions
Impact of Template Choice on Homology Model Efficiency in Virtual Screening
Learning To Predict Reaction Conditions: Relationships between Solvent, Molecular Structure, and Catalyst
SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses
Graph-Based Clustering of Predicted Ligand-Binding Pockets on Protein Surfaces
Benzenoid series having a constant number of isomers
Transfer Learning for Heterocycle Retrosynthesis
Deciphering the Morphological Difference of Amyloid-β Fibrils in Familial and Sporadic Alzheimer's Diseases
Three-Dimensional Quantitative Structure-Activity Relationships from Tuned Molecular Quantum Similarity Measures: Prediction of the Corticosteroid-Binding Globulin Binding Affinity for a Steroid Family
Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A
Critical Comparison of Virtual Screening Methods against the MUV Data Set