yusuke1997/dblp-id-title huggingface dataset:
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids
Information Systems for Optimum Use of Ocean Resources
Starting material oriented retrosynthetic analysis in the LHASA program. 3. Heuristic estimation of synthetic proximity
Pharmacophore-Based Virtual Screening and Experimental Validation of Novel Inhibitors against Cyanobacterial Fructose-1, 6-/Sedoheptulose-1, 7-bisphosphatase
Communication and Communities of Chemists
How Different Are Two Chemical Structures?
Exploration of Ultralarge Compound Collections for Drug Discovery
SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation
Investigation of Nascent Base Pair and Polymerase Behavior in the Presence of Mismatches in DNA Polymerase I Using Molecular Dynamics
Can you teach me to do my own searching? or tailoring online training to the needs of the end-user
Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations
Probabilistic Models for Capturing More Physicochemical Properties on Protein-Protein Interface
Adjusting Catalytic Activity of β-Amyrin Synthase GgBAS by Utilizing the Plasticity Residues of an Active Site
Nearest Neighbor Gaussian Process for Quantitative Structure-Activity Relationships
Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from Penaeus monodon : An In Silico Study through MD Simulations
Protein Surface Conservation in Binding Sites
Significant Enhancement of Docking Sensitivity Using Implicit Ligand Sampling
Integrative Data Mining, Scaffold Analysis, and Sequential Binary Classification Models for Exploring Ligand Profiles of Hepatic Organic Anion Transporting Polypeptides
Multisource Attention-Mechanism-Based Encoder-Decoder Model for Predicting Drug-Drug Interaction Events
Fast computation of the Wiener index of fasciagraphs and rotagraphs
Bayesian Algorithm for Retrosynthesis
Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum
Three-Dimensional Structure Database of Natural Metabolites (3DMET): A Novel Database of Curated 3D Structures
MTD-PLS: A PLS-Based Variant of the MTD Method, 2. Mapping Ligand-Receptor Interactions. Enzymatic Acetic Acid Esters Hydrolysis
Accurate Prediction of Enzyme Thermostabilization with Rosetta Using AlphaFold Ensembles
Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter
Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly
Enthalpy of Solvation Correlations for Gaseous Solutes Dissolved in Water and in 1-Octanol Based on the Abraham Model
Dynamic Behavior of Avian Influenza A Virus Neuraminidase Subtype H5N1 in Complex with Oseltamivir, Zanamivir, Peramivir, and Their Phosphonate Analogues
Fourth Indo-U.S. Workshop on Mathematical Chemistry, January 8-12, 2005, Pune, Maharashtra, India
Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation
One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space
Atomic Local Neighborhood Flexibility Incorporation into a Structured Similarity Measure for QSAR
The Playbooks of Medicinal Chemistry Design Moves
Visualization and Virtual Screening of the Chemical Universe Database GDB-17
Dielectric Polymer Property Prediction Using Recurrent Neural Networks with Optimizations
Computer-assisted infrared identification of vapor-phase mixture components
Idealized Models of Protofilaments of Human Islet Amyloid Polypeptide
Steered Molecular Dynamics Simulation in Rational Drug Design
Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning
Prediction of Aquatic Toxicity: Use of Optimization of Correlation Weights of Local Graph Invariants
Criteria of Quality Assessment for Scientific Databases
Ultrafast Algorithm for Designing Focused Combinational Arrays
Comment on the Definition and Labeling of p K 50
CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes
Flexible Alignment of Small Molecules Using the Penalty Method
Graphical Representation of Chemical Structures in Chemical Abstracts Service Publications
Comparative Molecular Field Analysis (CoMFA) of Anionic Azo Dye-Fiber Affinities I: Gas-Phase Molecular Orbital Descriptors
Precipitation at Equivalence and Equilibrium: A Method for the Determination of Equilibrium Constants of Reaction between Multideterminant Antigen and Specific Polyclonal Antibodies
Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling
Receptor-Based Virtual Ligand Screening for the Identification of Novel CDC25 Phosphatase Inhibitors
How E-, L-, and P-Selectins Bind to sLe x and PSGL-1: A Quantification of Critical Residue Interactions
scMDCL: A Deep Collaborative Contrastive Learning Framework for Matched Single-Cell Multiomics Data Clustering
RLpMIEC: High-Affinity Peptide Generation Targeting Major Histocompatibility Complex-I Guided and Interpreted by Interaction Spectrum-Navigated Reinforcement Learning
Comparative Study of Machine-Learning and Chemometric Tools for Analysis of In-Vivo High-Throughput Screening Data
Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS
Predicting Drug-Target Interaction Using a Novel Graph Neural Network with 3D Structure-Embedded Graph Representation
Properties of Star-Branched Polymer Brushes
Pcetk : A pDynamo-based Toolkit for Protonation State Calculations in Proteins
Selection of molecular fragment features for structure-activity studies in antitumor screening
Bit Silencing in Fingerprints Enables the Derivation of Compound Class-Directed Similarity Metrics
MacSpec and ConvertIt
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening
Design of Novel Rho Kinase Inhibitors Using Energy Based Pharmacophore Modeling, Shape-Based Screening, in Silico Virtual Screening, and Biological Evaluation
Predicted Biological Activity of Purchasable Chemical Space
A System for Encoding and Searching Markush Structures
Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps (LiCABEDS) and Its Application on Modeling Ligand Functionality for 5HT-Subtype GPCR Families
Estimation of Molecular Linear Free Energy Relationship Descriptors by a Group Contribution Approach. 2. Prediction of Partition Coefficients
Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods
IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors
Transition State Structure and Energetics of the N2O + X (X = Cl, Br) Reactions
Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?
A Comprehensive Approach to Argumentation
Application of microcomputer-based robust regression methods to nonlinear data analysis
ChemDataExtractor: A Toolkit for Automated Extraction of Chemical Information from the Scientific Literature
Behavior of Trapped Molecules in Lantern-Like Carcerand Superphanes
Breaking the Gender Imbalance: Female Presence in the Computational Chemistry Group at Viva Biotech
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?
Phase Transition and Phase Separation in Realistic Thylakoid Lipid Membrane of Marine Algae in All-Atom Simulations
Concept Design of Computer-Aided Study on Traditional Chinese Drugs
Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets
3D-QSAR and Molecular Mechanics Study for the Differences in the Azole Activity against Yeastlike and Filamentous Fungi and Their Relation to P450DM Inhibition. 1. 3-Substituted-4(3H)-quinazolinones
Combining 3-D Quantitative Structure-Activity Relationship with Ligand Based and Structure Based Alignment Procedures for in Silico Screening of New Hepatitis C Virus NS5B Polymerase Inhibitors
BB-SAR: An Application for Data-driven Analysis and Rational Design of Medicinal Chemistry Series
Deciphering the Allosteric Activation Mechanism of SIRT6 Using Molecular Dynamics Simulations
Atomistic Mechanism Underlying the Regulation of the GPA1 G Protein Signaling Pathway Mediated by the Gibberellin A1 Phytohormone Binding to the GCR1 Plant G-Protein-Coupled Receptor
Dynamic Heterogeneity at the Interface of an Intrinsically Disordered Peptide
BitClust: Fast Geometrical Clustering of Long Molecular Dynamics Simulations
Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors
A reasonable triamantane rearrangement path searched by the selective disource propagation algorithm
Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets
Design of Multitarget Activity Landscapes That Capture Hierarchical Activity Cliff Distributions
Hierarchical Deep Potential with Structure Constraints for Efficient Coarse-Grained Modeling
Response of Terahertz Protein Vibrations to Ligand Binding: Calmodulin-Peptide Complexes as a Case Study
A Multiscale Simulation Approach to Compute Protein-Ligand Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics
Predicting the Phosphorylation Sites Using Hidden Markov Models and Machine Learning Methods
Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine
QSAR and k-Nearest Neighbor Classification Analysis of Selective Cyclooxygenase-2 Inhibitors Using Topologically-Based Numerical Descriptors
An assessment of the carcinogenicity of N-nitroso compounds by the SIMCA method of pattern recognition
A comparison of three online Markush databases
Identification of Novel Inhibitors of Leishmania donovani γ-Glutamylcysteine Synthetase Using Structure-Based Virtual Screening, Docking, Molecular Dynamics Simulation, and in Vitro Studies
Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening
Information services providers: copyright issues for the eighties
Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase
Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study
Data Mining Approach for Extraction of Useful Information About Biologically Active Compounds from Publications
Upgrading Reliability in Molecular Property Prediction by Robust Quantification of Uncertainty from Machine Learning Models
Matched Molecular Series: Measuring SAR Similarity
ChemOffice Plus: A Package of Programs for Chemists
An Algorithm for Computing the Automorphism Group of Organic Structures with Stereochemistry and a Measure of its Efficiency
Parameterization and Conformational Sampling Effects in Pharmacophore Multiplet Searching
Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests
Extended Quality (eQual): Radial Threshold Clustering Based on n -ary Similarity
PRO_LIGAND: An Approach to de Novo Molecular Design, 5. Tools for the Analysis of Generated Structures
SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features
The third BASIC fragment search dictionary
Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst
Importance of Native-State Topology for Determining the Folding Rate of Two-State Proteins
Journals and conference proceedings of chemical history, education, and documentation
Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study
Underestimated Noncovalent Interactions in Protein Data Bank
Combinatorial Chemistry and Molecular Diversity in Drug Discovery Edited by Eric M. Gordon and James F. Kerwin, Jr.. Wiley-Liss: New York, 1998, 516 pp, ISBN 0-47-15518-7
Trends and Plot Methods in MLR Studies
Exploring the Active Center of the LSD1/CoREST Complex by Molecular Dynamics Simulation Utilizing Its Co-crystallized Co-factor Tetrahydrofolate as a Probe
DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs
Validation of the Generalized Force Fields GAFF, CGenFF, OPLS-AA, and PRODRGFF by Testing Against Experimental Osmotic Coefficient Data for Small Drug-Like Molecules
An Information-Based Computational Technique for Estimation of Chromatographic Peak Purity
Split Integration Symplectic Method for Molecular Dynamics Integration
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations
COVID19 - Computational Chemists Meet the Moment
Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation
Topological organic chemistry. 2. Graph theory, matrix determinants and eigenvalues, and topological indexes of alkanes
Why Are the Kinked Polyacenes More Stable than the Straight Ones? A Topological Study and Introduction of a New Topological Index of Aromaticity
Using Molecular Equivalence Numbers To Visually Explore Structural Features that Distinguish Chemical Libraries
Extraction of Information from the Text of Chemical Patents. 1. Identification of Specific Chemical Names
Whole-Molecule Calculation of Log P Based on Molar Volume, Hydrogen Bonds, and Simulated 13 C NMR Spectra
The NCI Drug Information System. 4. Inventory and shipping modules
An Unsupervised Machine Learning Approach for the Automatic Construction of Local Chemical Descriptors
Development of a Computational Tool to Rival Experts in the Prediction of Sites of Metabolism of Xenobiotics by P450s
A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis
A Novel Search Engine for Virtual Screening of Very Large Databases
Flexibility of the Binding Regions of a Protein-DNA Complex and the Structure and Ordering of Interfacial Water
Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps
Small-World Phenomena in Chemical Library Networks: Application to Fragment-Based Drug Discovery
X-ray Crystallographic Structures as a Source of Ligand Alignment in 3D-QSAR
Machine Learning-Guided Generation of Novel Pseudo-Natural Products: Applications to Accelerate Drug Discovery
Identification of New Fyn Kinase Inhibitors Using a FLAP-Based Approach
Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates
Computational Modeling of PROTAC Ternary Complexes as Ensembles Using SILCS-xTAC
Stochastic Algorithms for Maximizing Molecular Diversity
DeepAIPs-Pred: Predicting Anti-Inflammatory Peptides Using Local Evolutionary Transformation Images and Structural Embedding-Based Optimal Descriptors with Self-Normalized BiTCNs
MoleQCage: Geometric High-Throughput Screening for Molecular Caging Prediction
Optimization of an in Silico Protocol Using Probe Permeabilities to Identify Membrane Pan-Assay Interference Compounds
PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data
Prediction and Interpretable Visualization of Retrosynthetic Reactions Using Graph Convolutional Networks
Proposed Hydrogen-Bonding Index of Donor or Acceptor Reflecting Its Intrinsic Contribution to Hydrogen-Bonding Strength
CANCERLINE: A New NLM/NCI Data Base
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree
Byte Structure Variable Length Coding (BS-VLC): A New Specific Algorithm Applied in the Compression of Trajectories Generated by Molecular Dynamics
Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring
Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis
Chemical Function Queries for 3D Database Search
Calculation of Quantum-Mechanical Descriptors for QSPR at the DFT Level: Is It Necessary?
Prediction of pKa Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines
Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point Charges
Protocols for Bridging the Peptide to Nonpeptide Gap in Topological Similarity Searches
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology
Construction and Test of Ligand Decoy Sets Using MDock: Community Structure-Activity Resource Benchmarks for Binding Mode Prediction
Interactions and Stabilities of the UV RESISTANCE LOCUS8 (UVR8) Protein Dimer and Its Key Mutants
Validation of a Field-Based Ligand Screener Using a Novel Benchmarking Data Set for Assessing 3D-Based Virtual Screening Methods
Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides
LEDAW: An Integrated Software Suite with GUI for Automating Local Energy Decomposition Analysis of Molecular Interactions
Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα-DNA Complex
Exploring Cocrystallized Aromatic Cage Binders to Target Histone Methylation Reader Proteins
Exploring Chemical Reaction Space with Machine Learning Models: Representation and Feature Perspective
NA-DB: An Online Database of Nucleoside Analogues
Modeling the Octanol-Water Partition Coefficients by an Optimized Molecular Connectivity Index
Applications of degree distribution. 2. Construction and enumeration of isomers in the alkane series
MGRL-DDI: Multiview Graph Representation Learning for Accurate Drug-Drug Interaction Prediction
On the Use of Information Theory for Assessing Molecular Diversity
Multiscale Modeling Reveals the Cause of Surface Stress Change on Microcantilevers Due to Alkanethiol SAM Adsorption
Massive in Silico Study of Noble Gas Binding to the Structural Proteome
Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes
Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs
Clustering of chemical structures on the basis of two-dimensional similarity measures
Extraction and Analysis of Chemical Modification Patterns in Drug Development
Conserved Luminal C-Terminal Domain Dynamically Controls Interdomain Communication in Sarcolipin
A Linear Line Notation for Flow Patterns in the Chemical Industry
Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets
Legitimate Utilization of Large Descriptor Pools for QSPR/QSAR Models
Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery
Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent
New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces
SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual Screening and Clustering
Accelerated Protein Folding Using Greedy-Proximal A
In Silico Observation of the Conformational Opening of the Glutathione-Binding Site of Microsomal Prostaglandin E2 Synthase-1
Mining the ChEMBL Database: An Efficient Chemoinformatics Workflow for Assembling an Ion Channel-Focused Screening Library
Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein-Ligand Docking Results
The Information Chemist's View of the Patent Information Needs of Research Workers and Patent Attorneys
Comparison between CACon and CASIA Files for Development of New SDI Service in 1977
Differential Stability of Aurein 1.2 Pores in Model Membranes of Two Probiotic Strains
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2
Probing the Dynamic Nature of Water Molecules and Their Influences on Ligand Binding in a Model Binding Site
Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis
Building of Robust and Interpretable QSAR Classification Models by Means of the Rivality Index
Algorithm for selecting the parent structural unit of a ring-chain assembly
USP and the Development of Drug Standards
Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase
Comparative Assessment of Multiresponse Regression Methods for Predicting the Mechanisms of Toxic Action of Phenols
Use of Measured Residual Dipolar Couplings to Calculate Residual Dipolar Couplings for a Protein Structure: A Case Study Using Hen Egg-White Lysozyme
Vertex indexes of molecular graphs in structure-activity relationships: a study of the convulsant-anticonvulsant activity of barbiturates and the carcinogenicity of unsubstituted polycyclic aromatic hydrocarbons
Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome
GLMCyp: A Deep Learning-Based Method for CYP450-Mediated Reaction Site Prediction
C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins
Prediction of Transmembrane Proteins Based on the Continuous Wavelet Transform
Consensus versus Individual QSARs in Classification: Comparison on a Large-Scale Case Study
Molecular Basis of Linear Free Energy Relationships. The Nature of Inductive Effect in Aliphatic Series
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches
ACT! 2005
Discovery of Novel Histamine H4 and Serotonin Transporter Ligands Using the Topological Feature Tree Descriptor
Electronic van der Waals Surface Property Descriptors and Genetic Algorithms for Developing Structure-Activity Correlations in Olfactory Databases
Investing in the Future
Determinants of Oligonucleotide Selectivity of APOBEC3B
Correlation of the Melting Points of Potential Ionic Liquids (Imidazolium Bromides and Benzimidazolium Bromides) Using the CODESSA Program [ J. Chem. Inf. Comput. Sci . 42 , 225-231 (2002)]
Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities
Molecular Generative Model Based on an Adversarially Regularized Autoencoder
Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations
The Leu/Val 6.51 Side Chain of Cannabinoid Receptors Regulates the Binding Mode of the Alkyl Chain of Δ 9 -Tetrahydrocannabinol
A Fractal Approach for Selecting an Appropriate Bin Size for Cell-Based Diversity Estimation
A Computational Approach to the Study of the Binding Mode of Dual ACE/NEP Inhibitors
Meta-GTM: Visualization and Analysis of the Chemical Library Space
Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations
The Development of Target-Specific Machine Learning Models as Scoring Functions for Docking-Based Target Prediction
A QXP-Based Multistep Docking Procedure for Accurate Prediction of Protein-Ligand Complexes
Comprehensive Drug-Likeness Prediction Using a Pretrained Transformer Model and Multitask Learning
OPLS-Based Multiclass Classification and Data-Driven Interclass Relationship Discovery
Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations
Clustering Files of Chemical Structures Using the Fuzzy k -Means Clustering Method
Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks
FASTDock: A Pipeline for Allosteric Drug Discovery
Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model