yusuke1997/dblp-id-title huggingface dataset:
Computational Neural Networks in Conjunction with Principal Component Analysis for Resolving Highly Nonlinear Kinetics
TeachOpenCADD-KNIME: A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows
Computational Chemistry: A Way To Reach Spectroscopic and Thermodynamic Data for Exotic Compounds
Semantic dictionary for substructure matching of chemical structures with general descriptors
Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search
Global energy minimization by rotational energy embedding
Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis
Relative BAT: An Automated Tool for Relative Binding Free Energy Calculations by the Separated Topologies Approach
Three-Dimensional Quantitative Structure-Activity Relationship Analysis of the New Potent Sulfonylureas Using Comparative Molecular Similarity Indices Analysis
Exploring Chloride Selectivity and Halogenase Regioselectivity of the SalL Enzyme through Quantum Mechanical/Molecular Mechanical Modeling
DEPACT and PACMatch: A Workflow of Designing De Novo Protein Pockets to Bind Small Molecules
Machine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor
SimNano: A Trust Region Strategy for Large-Scale Molecular Systems Energy Minimization Based on Exact Second-Order Derivative Information
PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations
Electronic Structure Study of Thermal Intraconversions of Some Dicyclopenta-Fused Polycyclic Aromatic Compounds
Optimum Utilization of a Compound Collection or Chemical Library for Drug Discovery
Machine Learning Classification of Chirality and Optical Rotation Using a Simple One-Hot Encoded Cartesian Coordinate Molecular Representation
Holographic Neural Networks as Nonlinear Discriminants for Chemical Applications
Multiview Joint Learning-Based Method for Identifying Small-Molecule-Associated MiRNAs by Integrating Pharmacological, Genomics, and Network Knowledge
Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks
Retro-Leapfrog and Related Retro Map Operations
Identification of the Core Chemical Structure in SureChEMBL Patents
Deciphering Glutaminyl Cyclase Catalytic Pathways Enables Recognition of Anchor Pharmacophores for Inhibitor Discovery
Global Molecular Identification from Graphs. Neutral and Ionized Main-Group Diatomic Molecules
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure
Insights into Molecular Basis of Cytochrome P450 Inhibitory Promiscuity of Compounds
Molecular Self-Assembly Strategy for Encapsulation of an Amphipathic α-Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles
Independent Component Analysis Yields Chemically Interpretable Latent Variables in Multivariate Regression
Graph-Based Deep Learning Models for Thermodynamic Property Prediction: The Interplay between Target Definition, Data Distribution, Featurization, and Model Architecture
Molecular Shapes and Chirality
Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach
CRYSRC: A Generalized Chemical Information System Applied to a Structural Data File
Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity
Stable Cavitation Interferes with Aβ 16-22 Oligomerization
Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry
Boosting Tree-Assisted Multitask Deep Learning for Small Scientific Datasets
A Novel In Silico Approach to Drug Discovery via Computational Intelligence
Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study
Deep Learning-Based Imbalanced Data Classification for Drug Discovery
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization
TMB Finding Pipeline: Novel Approach for Detecting β-Barrel Membrane Proteins in Genomic Sequences
Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 - A Public Library of Challenging Docking Benchmark Sets
Modeling Lanthanide Coordination Complexes. Comparison of Semiempirical and Classical Methods
Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening
Comparison of conformations of small molecule structures from the Protein Data Bank with those generated by Concord, Cobra, ChemDBS-3D, and Converter and those extracted from the Cambridge Structural Database
Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature
The (Re)-Evolution of Quantitative Structure-Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods
Evaluating Chemical Structure Similarity as an Indicator of Cellular Growth Inhibition
Active Learning with Support Vector Machines in the Drug Discovery Process
Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules
Description of organic reactions based on imaginary transition structures. 3. Classification of one-string reactions having an odd-membered cyclic reaction graph
Fluor-Predictor: An Interpretable Tool for Multiproperty Prediction and Retrieval of Fluorescent Dyes
Stereo numbers, cosets, and the configuration symmetry group
Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points?
Predictive Modeling of High-Entropy Alloys and Amorphous Metallic Alloys Using Machine Learning
Multiclassification Prediction of Enzymatic Reactions for Oxidoreductases and Hydrolases Using Reaction Fingerprints and Machine Learning Methods
Practically Significant Method Comparison Protocols for Machine Learning in Small Molecule Drug Discovery
X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy
Building Block-Based Binding Predictions for DNA-Encoded Libraries
Protein-Ligand Docking Using Mutually Orthogonal Latin Squares (MOLSDOCK)
Frequency of even and odd numbers in distance matrixes of bipartite graphs
The Utilization of Reduced Dimensional Representations of Molecular Structure for Rapid Molecular Similarity Calculations
Factors Governing the Different Functions of Zn2+-Sites with Identical Ligands in Proteins
Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures
Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase
An Interpretable Multitask Framework BiLAT Enables Accurate Prediction of Cyclin-Dependent Protein Kinase Inhibitors
Quantitative Structure-Retention Relationship Models To Support Nontarget High-Resolution Mass Spectrometric Screening of Emerging Contaminants in Environmental Samples
Improving Trichoderma reesei Cel7B Thermostability by Targeting the Weak Spots
Incorporating chemical literature and information retrieval into the chemistry curriculum at the Hebrew University
Application of Large Language Models in Drug-Induced Osteotoxicity Prediction
Computational Design of Highly Selective Antimicrobial Peptides
Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide
Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes
Predicting the Genotoxicity of Secondary and Aromatic Amines Using Data Subsetting To Generate a Model Ensemble
Book Review of Molecular Design (Concepts and Applications)
Classical Molecular Dynamics with Mobile Protons
PiNN: A Python Library for Building Atomic Neural Networks of Molecules and Materials
Gas-Phase and Solution Conformations of the alpha-L-Iduronic Acid Structural Unit of Heparin
Automated Resonance Assignment of Proteins Using Heteronuclear 3D NMR, 2. Side Chain and Sequence-Specific Assignment
Prediction of HPLC Retention Index Using Artificial Neural Networks and IGroup E-State Indices
Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations
Distinct Modes of Action of IAPP Oligomers on Membranes
Error Detection, Recovery, and Repair in the Translation of Inorganic Nomenclatures, 3. An Error Handler
Molecular Dynamics-Ensemble Docking and Biophysical Studies for Structure-Based Identification of Non-Amino Acidic Ligands of DDAH-1
Molecular Mechanisms of the Blockage of Glioblastoma Motility
Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes
Computer Software Applications in Chemistry. By Peter C. Jurs. Second Edition. John Wiley & Sons, Inc.: New York, 1996, 291 pp, ISBN 0-471-10587-2
Permeability of Dermatological Solutes through the Short Periodicity Phase of Human Stratum Corneum Lipid Bilayers
Structural Dynamics of Lys11-Selective Deubiquitinylase Cezanne-1 during the Catalytic Cycle
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm
Fundamental Difference That Exists between Synthetic versus Analytic Chemical Nomenclature
Machine Learning Models Identify Inhibitors of SARS-CoV-2
Robotics In The Laboratory
Computational Study on the Interaction of N1 Substituted Pyrazole Derivatives with B-Raf Kinase: An Unusual Water Wire Hydrogen-Bond Network and Novel Interactions at the Entrance of the Active Site
Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces
Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE
Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches
A General Treatment of Solubility. 2. QSPR Prediction of Free Energies of Solvation of Specified Solutes in Ranges of Solvents
Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples
A Critical Comparison of Approximation Methods and Models for Equilibrium Properties of Low-Barrier Hydrogen Bonds
Employment of fuzzy information derived from spectroscopic data toward reducing the redundancy in the process of structure generation
Carborane Clusters in Computational Drug Design: A Comparative Docking Evaluation Using AutoDock, FlexX, Glide, and Surflex
Geometry Optimization Using the Frozen Domain and Partial Dimer Approaches in the Fragment Molecular Orbital Method: Implementation, Benchmark, and Applications to Protein Ligand-Binding Sites
InfVis - Platform-Independent Visual Data Mining of Multidimensional Chemical Data Sets
A relaxation algorithm for generic chemical structure screening
Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF 1 R as a Test Case
ZINC 15 - Ligand Discovery for Everyone
Degree Distance of a Graph: A Degree Analog of the Wiener Index
MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement
Three Useful Dimensions for Domain Applicability in QSAR Models Using Random Forest
Prediction of Aqueous Solubility of Heteroatom-Containing Organic Compounds from Molecular Structure
Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization
Information: New Questions to a Multidisciplinary Concept. Edited by Klaus Kornwachs and Konstantin Jacoby. Akademie Verlag GmbH: Berlin, 1996, 360 pp, ISBN 3-05-501665-3
First-Principle Calculation of Reduced Masses in Vibrational Analysis Using Generalized Internal Coordinates: Some Crucial Aspects and Examples
3D-Pharmacophore Models for Selective A 2A and A 2B Adenosine Receptor Antagonists
A Qualitative Comparison of Wiswesser Line Notation Descriptors of Reactions and the Derwent Chemical Reaction Documentation Service
Docking Validation Resources: Protein Family and Ligand Flexibility Experiments
Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein-Ligand to RNA-Ligand Binding
Distribution Analysis of the Variation of B-Factors of X-ray Crystal Structures: Temperature and Structural Variations in Lysozyme
Molecular Dynamics Studies of the STAT3 Homodimer: DNA Complex: Relationships between STAT3 Mutations and Protein-DNA Recognition
SEFLIN-Separate Feature Linear Notation System for Chemical Compounds
Hydration Thermodynamics of Familial Parkinson's Disease-Linked Mutants of α-Synuclein
How Beneficial Is Pretraining on a Narrow Domain-Specific Corpus for Information Extraction about Photocatalytic Water Splitting?
Developing a Transferable Coarse-Grained Model for the Prediction of Thermodynamic, Structural, and Mechanical Properties of Polyimides at Different Thermodynamic State Points
Mapping Monomeric Threading to Protein-Protein Structure Prediction
Neural Network-Topological Indices Approach to the Prediction of Properties of Alkene
Truncated Variants of the GCN4 Transcription Activator Protein Bind DNA with Dramatically Different Dynamical Motifs
Can 3D Structural Parameters Be Predicted from 2D (Topological) Molecular Descriptors?
Using Parallel Supercomputers To Calculate Surface Energy Distributions
Reason Vectors: Abstract Representation of Chemistry-Biology Interaction Outcomes, for Reasoning and Prediction
Structure/Response Correlations and Similarity/Diversity Analysis by GETAWAY Descriptors, 1. Theory of the Novel 3D Molecular Descriptors
Visualization of Regional Properties of Hardness and Softness in Molecules
Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules
The Vertex-Connectivity Index Revisited
Use of Experimental Design To Optimize Docking Performance: The Case of LiGenDock, the Docking Module of Ligen, a New De Novo Design Program
CASSI and the Compression of Journal Names in an Information Retrieval System
Development of a Reverse Phase HPLC Retention Index Model for Nontargeted Metabolomics Using Synthetic Compounds
Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model
Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer's Disease: Insights from Computational Chemistry Studies
Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling
Computer generation of Pauling bond orders using heuristic search
Application of Machine Learning in Spatial Proteomics
Prediction of Activity Cliffs Using Support Vector Machines
Selective Inhibition of STAT3 with Respect to STAT1: Insights from Molecular Dynamics and Ensemble Docking Simulations
Novel Method for Geometry Optimization of Molecular Clusters: Application to Benzene Clusters
Near-Term Quantum Classification Algorithms Applied to Antimalarial Drug Discovery
Assessment of a Novel Scoring Method Based on Solvent Accessible Surface Area Descriptors
Local and Global Quantitative Structure-Activity Relationship Modeling and Prediction for the Baseline Toxicity
Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease
Quantitative Structure-Activity Relationships for the Enantioselectivity of Oxirane Ring-Opening Catalyzed by Epoxide Hydrolases
Diameter Is a Key 3D Characteristic for Assessments of Efficient Inhibitors of Protein-Protein Interactions
Discovery of Novel Small Molecule Dual Inhibitor Targeting Toll-Like Receptors 7 and 9
Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction
Self-Learning Molecular Design for High Lithium-Ion Conductive Ionic Liquids using Maze Game
Discovery of a Novel and Potent LCK Inhibitor for Leukemia Treatment via Deep Learning and Molecular Docking
Classification of Current Scoring Functions
CONCORD and CAMBRIDGE: comparison of computer generated chemical structures with x-ray crystallographic data
TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations
How To Winnow Actives from Inactives: Introducing Molecular Orthogonal Sparse Bigrams (MOSBs) and Multiclass Winnow
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity
Navigating High-Dimensional Activity Landscapes: Design and Application of the Ligand-Target Differentiation Map
Activation Mechanism of the Human Histamine H4 Receptor - An Explicit Membrane Molecular Dynamics Simulation Study
ThermoData Engine (TDE) Software Implementation of the Dynamic Data Evaluation Concept. 7. Ternary Mixtures
Melting point and normal boiling point correlations: applications to rigid aromatic compounds
Probing Conformational Transition of TRPV5 Induced by Mechanical Force Using Coarse-Grained Molecular Dynamics
Doping Effects on the Performance of Paired Metal Catalysts for the Hydrogen Evolution Reaction
A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities
Investigation on the Mechanisms of Synchronous Interaction of K3Cit with Melamine and Uric Acid That Avoids the Formation of Large Clusters
ChemInform - an integrated information system on chemical reactions
Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points
Using Buriedness To Improve Discrimination between Actives and Inactives in Docking
A Highly Sensitive Model Based on Graph Neural Networks for Enzyme Key Catalytic Residue Prediction
BCMCMI: A Fusion Model for Predicting circRNA-miRNA Interactions Combining Semantic and Meta-path
Theoretical Scales of Hydrogen Bond Acidity and Basicity for Application in QSAR/QSPR Studies and Drug Design. Partitioning of Aliphatic Compounds
All That Glitters Is Not Gold: Importance of Rigorous Evaluation of Proteochemometric Models
Calculation of Aqueous Solubility of Crystalline Un-Ionized Organic Chemicals and Drugs Based on Structural Similarity and Physicochemical Descriptors
CAUTION: Popular "Benchmark" Data Sets Do Not Distinguish the Merits of 3D QSAR Methods
Luddite: An Information-Theoretic Library Design Tool
Switchable Nonlinear Optical Properties of η 5 -Monocyclopentadienylmetal Complexes: A DFT Approach
Computational Modeling of an Epidermal Growth Factor Receptor Single-Mutation Resistance to Cetuximab in Colorectal Cancer Treatment
On Topological Indices, Boiling Points, and Cycloalkanes
Maya 8 for Windows and Macintosh (Visual Quickstart Guide) By Morgan Robinson & Nathaniel Stern. Peachpit Press. 2007. xii + 532 pp. ISBN 0-321-47675-1, 978-0-321-47675-1. Softcover U.S. $34.99
Automated Extraction of Information from the Literature on Chemical-CYP3A4 Interactions
Classification of Substrates and Inhibitors of P-Glycoprotein Using Unsupervised Machine Learning Approach
Impact of Protein Conformational Diversity on Structure-Based Prediction of Druggability
Prediction of Solvation Free Energies of Small Organic Molecules: Additive-Constitutive Models Based on Molecular Fingerprints and Atomic Constants
Computer storage and retrieval of generic chemical structures in patents. 9. An algorithm to find the extended set of smallest rings in structurally explicit generics
Combined Pseudopotential and Density Functional Study of Bis-6-benzene d and f Element Complexes
Prediction of Ligand-Receptor Binding Free Energy by 4D-QSAR Analysis: Application to a Set of Glucose Analogue Inhibitors of Glycogen Phosphorylase
A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery
MetaMBP: Few-Shot Multilabel Prediction of Bioactive Peptides Based on Deep Metric Meta-Learning
Information Theory-Based Scoring Function for the Structure-Based Prediction of Protein-Ligand Binding Affinity
Conservative Electrostatic Potential Patterns at Enzyme Active Sites: The Anion-Cation-Anion Triad
Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities
An Efficient Design for Chemical Structure Searching. III. The Coding of Resonating and Tautomeric Forms
Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?
Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor
A Study on the Antipicornavirus Activity of Flavonoid Compounds (Flavones) by Using Quantum Chemical and Chemometric Methods
Multifingerprint Based Similarity Searches for Targeted Class Compound Selection
Alchemical Free Energy Calculations to Investigate Protein-Protein Interactions: the Case of the CDC42/PAK1 Complex
In Silico Studies toward the Discovery of New Anti-HIV Nucleoside Compounds with the Use of TOPS-MODE and 2D/3D Connectivity Indices, 1. Pyrimidyl Derivatives
Pharmacophore Features Distributions in Different Classes of Compounds
Ranking Molecules with Vanishing Kernels and a Single Parameter: Active Applicability Domain Included
Unresolved problems and opportunities in chemical literature teaching
Generalized Workflow for Generating Highly Predictive in Silico Off-Target Activity Models
Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints
Rule induction for systems predicting biological activity. [Erratum to document cited in CA120: 76590]
Shotgun Approach for PROTAC Ternary Complex Modeling and Evaluation
Design of a Rotamer Library for Coarse-Grained Models in Protein-Folding Simulations
Born-again FORTRAN: FORTRAN 77
Swarm Smart Meta-Estimator for 2D/2D Heterostructure Design
Docking Challenge: Protein Sampling and Molecular Docking Performance
Determination of the Free Energies of Mixing of Organic Solutions through a Combined Molecular Dynamics and Bayesian Statistics Approach
Development of Three-Dimensional Descriptors Represented by Tensors: Free Energy of Hydration Density Tensor
Atomic and Ion Collisions in Solids and at Surfaces. Theory, Simulation, and Applications. Roger Smith, Mario Jakas, Dave Ashworth, Bob Oven, Mark Bowyer, Ivan Chakarov, and Roger Webb. Cambridge University Press, 309 pp, 1997, ISBN 0-521-44022
Training Similarity Measures for Specific Activities: Application to Reduced Graphs
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge
Designing Compound Subsets: Comparison of Random and Rational Approaches Using Statistical Simulation
Learning Chemistry of Complex Reaction Systems via a Python First-Principles Reaction Rule Stencil (pReSt) Generator
Classification of chemical reactions: potential, possibilities and continuing relevance
Chemical Inference Based on SEFLIN. I. Basic Cognizance of Molecular Shape, Fragments, Atomic Environment of Organic Compounds
Predictive Model of Linear Antimicrobial Peptides Active against Gram-Negative Bacteria
Molecular Symmetry Perception
A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016
TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction
Conformational Signatures of Preassembled and Active Complexes of 5-HT 7 with the G s Protein
Improving Similarity-Driven Library Design: Customized Matching and Regioselective Feature Trees
Template CoMFA Applied to 116 Biological Targets
SparcleQC: Automated Input File Creation for QM/MM Studies of Protein:Ligand Complexes
Some Open Mathematical Problems on Fullerenes
Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric
Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA-Ligand Poses?
Accord for Excel
Dimerization Behavior of Methyl Chlorophyllide a as the Model of Chlorophyll a in the Presence of Water Molecules - Theoretical Study
Understanding the Binding Specificity of G-Protein Coupled Receptors toward G-Proteins and Arrestins: Application to the Dopamine Receptor Family
On Calculation of the Detour Index
Robust Quantum Reservoir Learning for Molecular Property Prediction
REACCS in the chemical development environment. 3. Graphically nonequivalent representations of molecules and reactions
Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation
Lipid Shape as a Membrane Activity Modulator of a Fusogenic Antimicrobial Peptide