Journal of Chemical Information and Modeling

Papers
(The median citation count of Journal of Chemical Information and Modeling is 4. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)
ArticleCitations
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings1636
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance464
ZINC20—A Free Ultralarge-Scale Chemical Database for Ligand Discovery335
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery187
REINVENT 2.0: An AI Tool for De Novo Drug Design175
TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials150
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects143
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference137
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction130
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19128
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation128
Rigorous Free Energy Simulations in Virtual Screening117
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function115
Assessment of Binding Affinity via Alchemical Free-Energy Calculations114
MolGPT: Molecular Generation Using a Transformer-Decoder Model114
SARS-CoV-2 Main Protease: A Molecular Dynamics Study113
Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease113
Machine Learning Meets with Metal Organic Frameworks for Gas Storage and Separation106
PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes106
Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations100
Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design100
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation100
Artificial Intelligence in Chemistry: Current Trends and Future Directions89
AmberTools88
Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis88
Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure–Activity Relationship Studies86
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations84
MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network83
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models83
Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine83
Generative Network Complex for the Automated Generation of Drug-like Molecules81
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)80
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies80
iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides79
PI1M: A Benchmark Database for Polymer Informatics77
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease76
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta72
Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling70
Evolution of Alchemical Free Energy Methods in Drug Discovery70
Benchmarking Machine Learning Models for Polymer Informatics: An Example of Glass Transition Temperature69
Deep Learning-Based Imbalanced Data Classification for Drug Discovery68
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning67
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro67
Recent Force Field Strategies for Intrinsically Disordered Proteins64
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy64
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning64
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro63
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields62
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides62
Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations59
Generative Deep Learning for Targeted Compound Design59
Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations59
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate57
De Novo Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization56
RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks56
Accelerating De Novo Drug Design against Novel Proteins Using Deep Learning56
N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study55
General Protocol for the Accurate Prediction of Molecular 13C/1H NMR Chemical Shifts via Machine Learning Augmented DFT54
Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations54
Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction53
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro53
Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles53
Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape53
BBPpred: Sequence-Based Prediction of Blood-Brain Barrier Peptides with Feature Representation Learning and Logistic Regression52
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning52
SMILES to Smell: Decoding the Structure–Odor Relationship of Chemical Compounds Using the Deep Neural Network Approach52
Exploration of Ultralarge Compound Collections for Drug Discovery52
Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits51
Computational Methods and Tools in Antimicrobial Peptide Research51
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro50
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor50
Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins50
IAMPE: NMR-Assisted Computational Prediction of Antimicrobial Peptides49
Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment48
Property-Unmatched Decoys in Docking Benchmarks48
Program Package for the Calculation of Origin-Independent Electron Current Density and Derived Magnetic Properties in Molecular Systems48
ChemDataExtractor 2.0: Autopopulated Ontologies for Materials Science47
tmQM Dataset—Quantum Geometries and Properties of 86k Transition Metal Complexes47
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations46
Exposing the Limitations of Molecular Machine Learning with Activity Cliffs45
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease45
What Are the Odds of Finding a COVID-19 Drug from a Lab Repurposing Screen?45
XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties44
GGL-Tox: Geometric Graph Learning for Toxicity Prediction44
Making it Rain: Cloud-Based Molecular Simulations for Everyone43
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design43
xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning43
Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation43
Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning43
Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a43
Informatics for Chemistry, Biology, and Biomedical Sciences43
OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design43
OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery43
SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning42
Quantum Machine Learning Algorithms for Drug Discovery Applications42
DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method42
A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters42
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks41
Prediction of Energetic Material Properties from Electronic Structure Using 3D Convolutional Neural Networks41
Improving the Performance of MM/PBSA in Protein–Protein Interactions via the Screening Electrostatic Energy41
DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks40
Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein–Protein Docking, Molecular Dynamics, and MM-GBSA Calculations40
SolTranNet–A Machine Learning Tool for Fast Aqueous Solubility Prediction39
De Novo Molecule Design Through the Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites39
AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges39
Lean-Docking: Exploiting Ligands’ Predicted Docking Scores to Accelerate Molecular Docking39
DeepBSP—a Machine Learning Method for Accurate Prediction of Protein–Ligand Docking Structures39
Interaction Nature and Computational Methods for Halogen Bonding: A Perspective39
AMPGAN v2: Machine Learning-Guided Design of Antimicrobial Peptides38
Structural and Dynamic Insights into Redundant Function of YTHDF Proteins38
Molassembler: Molecular Graph Construction, Modification, and Conformer Generation for Inorganic and Organic Molecules38
Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening38
Systematic Investigation of the Data Set Dependency of Protein Stability Predictors38
Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD38
Guidelines for Recurrent Neural Network Transfer Learning-Based Molecular Generation of Focused Libraries38
Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-137
PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties37
BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations37
Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning37
Enabling High-Throughput Searches for Multiple Chemical Data Using the U.S.-EPA CompTox Chemicals Dashboard37
Multilabel Classification Models for the Prediction of Cross-Coupling Reaction Conditions37
Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study37
A General Picture of Cucurbit[8]uril Host–Guest Binding37
Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity37
Prediction of Natural Product Classes Using Machine Learning and 13C NMR Spectroscopic Data37
PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations36
Molcontroller: A VMD Graphical User Interface Featuring Molecule Manipulation36
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery36
Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods36
Predicting Infrared Spectra with Message Passing Neural Networks35
Practical Applications of Deep Learning To Impute Heterogeneous Drug Discovery Data35
Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions35
NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering35
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models35
Chemistry42: An AI-Driven Platform for Molecular Design and Optimization35
In Silico Screening-Based Discovery of Novel Inhibitors of Human Cyclic GMP–AMP Synthase: A Cross-Validation Study of Molecular Docking and Experimental Testing35
A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry34
Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics34
Structural Assessment of Agonist Efficacy in the μ-Opioid Receptor: Morphine and Fentanyl Elicit Different Activation Patterns34
Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes34
ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning34
Do Large Language Models Understand Chemistry? A Conversation with ChatGPT34
Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites33
mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria33
Structure-Aware Multimodal Deep Learning for Drug–Protein Interaction Prediction33
Combining Cloud-Based Free-Energy Calculations, Synthetically Aware Enumerations, and Goal-Directed Generative Machine Learning for Rapid Large-Scale Chemical Exploration and Optimization33
Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations33
Machine Learning Directed Optimization of Classical Molecular Modeling Force Fields32
Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients32
New Trends in Virtual Screening32
RMG Database for Chemical Property Prediction32
Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: the Main Protease (Mpro) Case Study32
Scaffold-Constrained Molecular Generation32
ADME Prediction with KNIME: Development and Validation of a Publicly Available Workflow for the Prediction of Human Oral Bioavailability32
GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds32
A Consistent Scheme for Gradient-Based Optimization of ProteinLigand Poses31
Prediction of Molecular Electronic Transitions Using Random Forests31
Findings of the Second Challenge to Predict Aqueous Solubility31
Improving Few- and Zero-Shot Reaction Template Prediction Using Modern Hopfield Networks31
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease31
Machine Learning Models Identify Inhibitors of SARS-CoV-231
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein–Ligand Scoring Functions30
Valid, Plausible, and Diverse Retrosynthesis Using Tied Two-Way Transformers with Latent Variables30
Predicting Energetics Materials’ Crystalline Density from Chemical Structure by Machine Learning30
True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better30
Extending the Martini Coarse-Grained Force Field to N-Glycans30
Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis30
Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the “Big Data” Era30
Improving Enzyme Optimum Temperature Prediction with Resampling Strategies and Ensemble Learning30
Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction30
Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates30
Comparative Study of Deep Generative Models on Chemical Space Coverage30
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning30
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease30
Search for ABO3 Type Ferroelectric Perovskites with Targeted Multi-Properties by Machine Learning Strategies30
Pathway-Guided Deep Neural Network toward Interpretable and Predictive Modeling of Drug Sensitivity30
Explainable Deep Relational Networks for Predicting Compound–Protein Affinities and Contacts29
Automated Chemical Reaction Extraction from Scientific Literature29
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models29
Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies29
Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery29
Dielectric Polymer Property Prediction Using Recurrent Neural Networks with Optimizations29
Deep Learning-Based Conformal Prediction of Toxicity29
VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein–Ligand Binding Free Energy Calculations29
LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design29
BatteryBERT: A Pretrained Language Model for Battery Database Enhancement28
Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server28
Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex28
Fast Estimation of the Blood–Brain Barrier Permeability by Pulling a Ligand through a Lipid Membrane28
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 Profil28
Kernel Methods for Predicting Yields of Chemical Reactions28
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design28
Cyclosporin A: Conformational Complexity and Chameleonicity28
Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast28
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions28
SGTPy: A Python Code for Calculating the Interfacial Properties of Fluids Based on the Square Gradient Theory Using the SAFT-VR Mie Equation of State28
Ligand Strain Energy in Large Library Docking28
Mining Insights on Metal–Organic Framework Synthesis from Scientific Literature Texts27
Applications of Machine Learning to In Silico Quantification of Chemicals without Analytical Standards27
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations27
Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures27
General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps27
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-1927
Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set27
Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations27
Prediction of Protein–Ligand Binding Pose and Affinity Using the gREST+FEP Method27
Predicting Protein–Ligand Docking Structure with Graph Neural Network26
De Novo Structure-Based Drug Design Using Deep Learning26
Density Prediction Models for Energetic Compounds Merely Using Molecular Topology26
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER26
Drug Repurposing to Identify Nilotinib as a Potential SARS-CoV-2 Main Protease Inhibitor: Insights from a Computational and In Vitro Study26
Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity26
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern26
Artificial Intelligence in Drug Toxicity Prediction: Recent Advances, Challenges, and Future Perspectives26
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models26
Misfolding and Self-Assembly Dynamics of Microtubule-Binding Repeats of the Alzheimer-Related Protein Tau26
MoleGuLAR: Molecule Generation Using Reinforcement Learning with Alternating Rewards26
Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics26
cgbind: A Python Module and Web App for Automated Metallocage Construction and Host–Guest Characterization26
Classification Model for the Second Extracellular Loop of Class A GPCRs26
In Silico Classifiers for the Assessment of Drug Proarrhythmicity26
Enhancing Hit Discovery in Virtual Screening through Absolute Protein–Ligand Binding Free-Energy Calculations25
Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening25
Effect of the Generation of PAMAM Dendrimers on the Stabilization of Gold Nanoparticles25
Selecting Collective Variables and Free-Energy Methods for Peptide Translocation across Membranes25
CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids25
Generative Chemical Transformer: Neural Machine Learning of Molecular Geometric Structures from Chemical Language via Attention25
Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning25
Diversity and Chemical Library Networks of Large Data Sets25
Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes25
Interpretation of Structure–Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence24
R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study24
Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus24
Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides24
Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening24
grand: A Python Module for Grand Canonical Water Sampling in OpenMM24
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method24
Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus24
FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method24
BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization24
Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design24
A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery24
Discovery of a New Donepezil-like Acetylcholinesterase Inhibitor for Targeting Alzheimer’s Disease: Computational Studies with Biological Validation24
ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields23
ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid–Ligand Interactions23
Is Structure-Based Drug Design Ready for Selectivity Optimization?23
Deep Learning Total Energies and Orbital Energies of Large Organic Molecules Using Hybridization of Molecular Fingerprints23
The (Re)-Evolution of Quantitative Structure–Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods23
Topological Similarity Search in Large Combinatorial Fragment Spaces23
PyRMD: A New Fully Automated AI-Powered Ligand-Based Virtual Screening Tool23
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