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2026
SLAB: simultaneous labeling and binding affinity prediction for protein–ligand structures
Digital Discovery
2025
Graph Neural Networks for Neurological Disorders
2025
Integrating Deep Learning and Molecular Dynamics to Identify GPR17 Ligands for Glioblastoma Therapy
Current Chemical Biology
2025
Protein-ligand binding affinity prediction using multi-instance learning with docking structures
Frontiers in Pharmacology
2025
A beginner’s approach to deep learning applied to VS and MD techniques
Journal of Cheminformatics
2025
Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design
Molecular Biotechnology
2025
PLAIG: Protein–Ligand Binding Affinity Prediction Using a Novel Interaction-Based Graph Neural Network Framework
ACS Bio & Med Chem Au
2025
Lecture Notes in Networks and Systems
2025
StructureNet: Physics-Informed Hybridized Deep Learning Framework for Protein–Ligand Binding Affinity Prediction
Bioengineering
2024
Prediction of protein–ligand binding affinity via deep learning models
Briefings in Bioinformatics
2024
Identifying Potent Fat Mass and Obesity-Associated Protein Inhibitors Using Deep Learning-Based Hybrid Procedures
BioMedInformatics
2024
ProBAN: Neural network algorithm for predicting binding affinity in protein–protein complexes
Proteins: Structure, Function, and Bioinformatics
2024
Computational Drug Discovery
2024
Advances in Deep Learning Assisted Drug Discovery Methods: A Self-review
Current Bioinformatics
2024
A comprehensive review of the recent advances on predicting drug-target affinity based on deep learning
Frontiers in Pharmacology
2024
Revolutionizing GPCR–ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery
Briefings in Bioinformatics
2024
Toward generalizable structure‐based deep learning models for protein–ligand interaction prediction: Challenges and strategies
WIREs Computational Molecular Science
2023
Does protein pretrained language model facilitate the prediction of protein–ligand interaction?
Methods
2023
Heterogeneous graph convolutional neural network for protein-ligand scoring
Exploration of Drug Science
2023
Binding affinity predictions with hybrid quantum-classical convolutional neural networks
Scientific Reports
2023
Structure‐Based Drug Discovery with Deep Learning**
ChemBioChem
2023
New Insights into the Cooperativity and Dynamics of Dimeric Enzymes
Chemical Reviews
2023
A normalized differential sequence feature encoding method based on amino acid sequences
Mathematical Biosciences and Engineering
2023
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15
Proteins: Structure, Function, and Bioinformatics
2023
Studies in Computational Intelligence
2023
Deep Learning Model for Efficient Protein–Ligand Docking with Implicit Side-Chain Flexibility
Journal of Chemical Information and Modeling
2023
DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Protein–Ligand Interaction Prediction
Molecules
2023
Drug Design and Disease Diagnosis: The Potential of Deep Learning Models in Biology
Current Bioinformatics
2023
Recent Developments in Ultralarge and Structure-Based Virtual Screening Approaches
Annual Review of Biomedical Data Science
2023
GRA-GCN: Dense Granule Protein Prediction in Apicomplexa Protozoa Through Graph Convolutional Network
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2022
On the Frustration to Predict Binding Affinities from Protein–Ligand Structures with Deep Neural Networks
Journal of Medicinal Chemistry
2022
A New Hybrid Neural Network Deep Learning Method for Protein–Ligand Binding Affinity Prediction and De Novo Drug Design
International Journal of Molecular Sciences
2022
Soil Moisture Content Estimation Based on Sentinel-1 SAR Imagery Using an Artificial Neural Network and Hydrological Components
Remote Sensing
2022
2022 IEEE International Conference on Big Data (Big Data)
2022
Hybrid drug-screening strategy identifies potential SARS-CoV-2 cell-entry inhibitors targeting human transmembrane serine protease
Structural Chemistry
2022
Machine learning in postgenomic biology and personalized medicine
WIREs Data Mining and Knowledge Discovery
2022
Active Site Sequence Representations of Human Kinases Outperform Full Sequence Representations for Affinity Prediction and Inhibitor Generation: 3D Effects in a 1D Model
Journal of Chemical Information and Modeling
2022
Communications in Computer and Information Science
2022
Sfcnn: a novel scoring function based on 3D convolutional neural network for accurate and stable protein–ligand affinity prediction
BMC Bioinformatics
2022
PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications
Scientific Data
2022
Emerging role of artificial intelligence in therapeutics for COVID-19: a systematic review
Journal of Biomolecular Structure and Dynamics
2022
Molecular modeling and dynamics studies of the synthetic small molecule agonists with GPR17 and P2Y1 receptor
Journal of Biomolecular Structure and Dynamics
2022
An Efficient Modern Strategy to Screen Drug Candidates Targeting RdRp of SARS-CoV-2 With Potentially High Selectivity and Specificity
Frontiers in Chemistry
2022
Protein Function Analysis through Machine Learning
Biomolecules
2022
DeepBindBC: A practical deep learning method for identifying native-like protein-ligand complexes in virtual screening
Methods
2022
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel–Ligand Docking
Journal of Chemical Information and Modeling
2022
Botanical drugs: a new strategy for structure-based target prediction
Briefings in Bioinformatics
2022
A point cloud-based deep learning strategy for protein–ligand binding affinity prediction
Briefings in Bioinformatics
2022
Biomedical Data and Deep Learning Computational Models for Predicting Compound-Protein Relations
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2021
An Integrated Deep Learning and Molecular Dynamics Simulation-Based Screening Pipeline Identifies Inhibitors of a New Cancer Drug Target TIPE2
Frontiers in Pharmacology
2021
Deep Learning in Virtual Screening: Recent Applications and Developments
International Journal of Molecular Sciences
2021
Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions
Briefings in Bioinformatics
2021
SMMPPI: a machine learning-based approach for prediction of modulators of protein–protein interactions and its application for identification of novel inhibitors for RBD:hACE2 interactions in SARS-CoV-2
Briefings in Bioinformatics
2021
From Drug Molecules to Thermoset Shape Memory Polymers: A Machine Learning Approach
ACS Applied Materials & Interfaces
2021
Methods in Pharmacology and Toxicology
2021
2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2021
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction
Bioinformatics
2021
Carbohydrate-Based NK1R Antagonists with Broad-Spectrum Anticancer Activity
Journal of Medicinal Chemistry
2021
Molecular Docking for Computer-Aided Drug Design
2021
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
2021
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference
Journal of Chemical Information and Modeling
2021
Recent trends in artificial intelligence-driven identification and development of anti-neurodegenerative therapeutic agents
Molecular Diversity
2020
Implementation of adaptive integration method for free energy calculations in molecular systems
PeerJ Computer Science
2020
Insight into potent leads for alzheimer's disease by using several artificial intelligence algorithms
Biomedicine & Pharmacotherapy
2020
Similarity-Based Methods and Machine Learning Approaches for Target Prediction in Early Drug Discovery: Performance and Scope
International Journal of Molecular Sciences
2020
Deep learning model predicts water interaction sites on the surface of proteins using limited-resolution data
Chemical Communications
2020
AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks
International Journal of Molecular Sciences
2020
Rapid Identification of Potential Inhibitors of SARS‐CoV‐2 Main Protease by Deep Docking of 1.3 Billion Compounds
Molecular Informatics
2020
Targeting the C-Terminal Domain Small Phosphatase 1
Life
2020
DeepBindPoc: a deep learning method to rank ligand binding pockets using molecular vector representation
PeerJ
2020
DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina
International Journal of Molecular Sciences
2020
Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov
Interdisciplinary Sciences: Computational Life Sciences
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