Journal of Chemical Information and Modeling

Article	Citations
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	3393
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	698
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	525
Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach	239
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	195
Lipid Oxidation: Role of Membrane Phase-Separated Domains	175
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	167
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	164
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	158
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains	147
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	124
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	118
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	116
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	115
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	106
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids	103
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications	102
Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis	102
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	97
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	93
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	91
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	90
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	89
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	88
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	86

Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis	85
HSQC Spectra Simulation and Matching for Molecular Identification	81
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	80
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	80
Issue Publication Information	79
The Often-Overlooked Power of Summary Statistics in Exploratory Data Analysis: Comparison of Pattern Recognition Entropy (PRE) to Other Summary Statistics and Introduction of Divided Spectrum-PRE (DS-	79
Issue Publication Information	77
Diffusion Models in De Novo Drug Design	77
Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19	75
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	71
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	69
Large Language Model for Automating the Analysis of Cryoprotectants	69
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design	68
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	68
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	68
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	67
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	66
Issue Publication Information	65
Issue Editorial Masthead	64
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19	63
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	63
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	63
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	63
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease	61
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	60
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	60
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	59
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	59
Analysis of Binding Modes of Antigen–Antibody Complexes by Molecular Mechanics Calculation	58
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	58
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	58
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	57
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	56
QM/MM Study of the Metabolic Oxidation of 6′,7′-Dihydroxybergamottin Catalyzed by Human CYP3A4: Preferential Formation of the γ-Ketoenal Product in Mechanism-Based Inactivation	56
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	55
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	55
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	55
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	55
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	54
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	54
Cyclosporin A: Conformational Complexity and Chameleonicity	54
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	54
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	52
QSAR Modeling Based on Conformation Ensembles Using a Multi-Instance Learning Approach	51
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	51
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	51
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	51
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	50
Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis	49
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	49

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	49
Integrated Approach to Identify Selective PTP1B Inhibitors Targeting the Allosteric Site	49
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	48
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	48
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	48
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	47
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	47
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight	47
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	47
Spatially Resolved Uncertainties for Machine Learning Potentials	47
Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations	46
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	46
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	46
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	45
Predicting the Likelihood of Molecules to Act as Modulators of Protein–Protein Interactions	44
Issue Editorial Masthead	44
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	43
Issue Publication Information	43
Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set	43
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	42
Locating Multiple Transition Pathways for Complex Biomolecules	42
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations	41
Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method	41
Rational Design of Nonbonded Point Charge Models for Divalent Metal Cations with Lennard-Jones 12-6 Potential	41
Multiple Interactions of Glucose with the Extra-Membranous Loops of GLUT1 Aid Transport	41
PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop	41
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison	41
Knowledge-Based Artificial Intelligence System for Drug Prioritization	41
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	40
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	40
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	40
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern	40
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	40
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	40
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	39
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	39
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	38
Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder	38
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	38
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	38
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	38
xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning	38
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	38
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	37
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	37
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	37
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	37
Atomic Polarizabilities for Interactive Dipole Induction Models	37
Study on the Assembly Mechanisms and Transport Properties of Transmembrane End-Charged Cyclic Peptide Nanotubes	37
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	37
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	37
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	36
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	36
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	36
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	36
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	36
First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach	35
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	35
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	35
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	35
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	35
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	35
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	35
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	35
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	34
Correction to “XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties”	34
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	34
Special Issue on Reaction Informatics and Chemical Space	34
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	34
Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment	34
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	33
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	33
QM/MM Study of Human Transketolase: Thiamine Diphosphate Activation Mechanism and Complete Catalytic Cycle	33
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	32
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW	32
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	32
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	32
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches	32
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	32
Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms	32

Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	32
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	32
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	31
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	31
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	31
Discovery of P2Y2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening	31
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	31
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures	31
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	31
af3cli: Streamlining AlphaFold3 Input Preparation	31
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	31
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation	31
Large Language Models as Tools for Molecular Toxicity Prediction: AI Insights into Cardiotoxicity	30
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches	30
Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity	30
KUTE: Green–Kubo Uncertainty-Based Transport Coefficient Estimator	30
Insights on Rigidity and Flexibility at the Global and Local Levels of Protein Structures and Their Roles in Homologous Psychrophilic, Mesophilic, and Thermophilic Proteins: A Computational Study	30
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides	30
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	29
Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease	29
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine	29
Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM	29
Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking	29
Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor	29
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions	29
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System	29
Kick–Fukui: A Fukui Function-Guided Method for Molecular Structure Prediction	29
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design	29
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin	29
Clustering of Synthetic Routes Using Tree Edit Distance	28
Large-Scale Modeling of Sparse Protein Kinase Activity Data	28
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction	28
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex	28
Activity Regulation and Conformation Response of Janus Kinase 3 Mediated by Phosphorylation: Exploration from Correlation Network Analysis and Markov Model	28
All-Atom Membrane Builder via Multiscale Simulation	28
De Novo Molecule Design Through the Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites	28
Large-Scale Distributed Training of Transformers for Chemical Fingerprinting	28
NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface	28
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs	28
Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function	28
Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study	27
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents	27
Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations	27
Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors	27
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios	27
Modeling the Structure–Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein	27
SMICLR: Contrastive Learning on Multiple Molecular Representations for Semisupervised and Unsupervised Representation Learning	27
OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions	27
Fast Prediction of Lipophilicity of Organofluorine Molecules: Deep Learning-Derived Polarity Characters and Experimental Tests	27
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2	27
Preventing AI From Creating Biochemical Threats	27
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs	27
Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus	26
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	26
Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study	26
ReactionDataExtractor 2.0: A Deep Learning Approach for Data Extraction from Chemical Reaction Schemes	26
Exploring the Potential of Adaptive, Local Machine Learning in Comparison to the Prediction Performance of Global Models: A Case Study from Bayer’s Caco-2 Permeability Database	26
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	26
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition	26
Issue Publication Information	26
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	26
Equivariant Graph-Representation-Based Actor–Critic Reinforcement Learning for Nanoparticle Design	26
AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro	26
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein	26
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes	25
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study	25
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids	25
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction	25
Issue Publication Information	25
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	25
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures	25
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations	25
Exploring the Substrate-Assisted Dehydration of Chorismate Catalyzed by Dehydratase MqnA from QM/MM Calculations: The Role of Pocket Residues and the Hydrolysis Mechanism of N17D Mutant	25
Issue Editorial Masthead	25
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	25
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies	25
Computer-Aided Design and Synthesis of a New Class of PEX14 Inhibitors: Substituted 2,3,4,5-Tetrahydrobenzo[F][1,4]oxazepines as Potential New Trypanocidal Agents	25
Issue Editorial Masthead	24
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	24
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	24
MPpredictor: An Artificial Intelligence-Driven Web Tool for Composition-Based Material Property Prediction	24
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort	24
Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations	24
Issue Publication Information	24
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations	24
Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes	24
Issue Editorial Masthead	24
Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation	24
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework	24
A Decade of Indonesian Atmosphere in Computer-Aided Drug Design	23
Chemprop: A Machine Learning Package for Chemical Property Prediction	23
COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework	23
Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes	23
Probing Allosteric Regulation Mechanism of W7.35 on Agonist-Induced Activity for μOR by Mutation Simulation	23
Issue Editorial Masthead	23