Papers Molecular Docking
“Molecular Docking” 태그가 달린 논문 128편 · 필터 해제
CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions
Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are partic…
BenchmarkingDrug DesignMolecular DockingPocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning
Sampling physically valid ligand-binding poses remains a major challenge in molecular docking, particularly for unseen or structurally diverse targets. We introduce PocketVina, a fast and memory-efficient, search-based d…
BenchmarkingDrug DiscoveryGPUMolecular Docking+1ReassembleNet: Learnable Keypoints and Diffusion for 2D Fresco Reconstruction
The task of reassembly is a significant challenge across multiple domains, including archaeology, genomics, and molecular docking, requiring the precise placement and orientation of elements to reconstruct an original st…
Molecular DockingPose EstimationMulti-Ligand Simultaneous Docking Analysis of Moringa Oleifera Phytochemicals Reveals Enhanced BCL-2 Inhibition via Synergistic Action
Moringa oleifera, known for its medicinal properties, contains bioactive compounds such as polyphenols and flavonoids with diverse therapeutic potentials, including anti-cancer effects. This study investigates the effica…
Molecular DockingPrediction of Novel CXCR7 Inhibitors Using QSAR Modeling and Validation via Molecular Docking
CXCR7, a G-protein-coupled chemokine receptor, has recently emerged as a key player in cancer progression, particularly in driving angiogenesis and metastasis. Despite its significance, currently, few effective inhibitor…
Molecular DockingComputational Analysis using Multi-ligand Simultaneous Docking of Withaferin A and Garcinol Reveals Enhanced BCL-2 and AKT-1 Inhibition
Developing an effective medicine to combat cancer and elusive stem cells is crucial in the current scenario. Withaferin A and Garcinol, important phytoconstituents of Withania somnifera (Ashwagandha) and Garcinia indica …
Molecular DockingIn Silico Prediction and Validation of LmGt Inhibitors Using QSAR and Molecular Docking Approaches
Leishmaniasis caused by Leishmania mexicana relies on Leishmania mexicana gluscose transporter (LmGT) receptors, which play an important role in glucose and ribose uptake at different stages of parasite's life cycle. Pre…
Drug DiscoveryMolecular DockingSpecificityEnhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning
Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces t…
Drug DesignDrug DiscoveryLanguage ModelingLanguage Modelling+3PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking
Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications. Moreover, some studies involve heavy frameworks requiring extensive training, posing cha…
Blind DockingMolecular DockingFast and Accurate Blind Flexible Docking
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either over…
Blind DockingComputational EfficiencyDrug DiscoveryMolecular Docking+1Generative Modeling on Lie Groups via Euclidean Generalized Score Matching
We extend Euclidean score-based diffusion processes to generative modeling on Lie groups. Through the formalism of Generalized Score Matching, our approach yields a Langevin dynamics which decomposes as a direct sum of L…
Molecular DockingDocking-Aware Attention: Dynamic Protein Representations through Molecular Context Integration
Computational prediction of enzymatic reactions represents a crucial challenge in sustainable chemical synthesis across various scientific domains, ranging from drug discovery to materials science and green chemistry. Th…
Drug DiscoveryMolecular DockingPredictionGroup Ligands Docking to Protein Pockets
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand …
Blind DockingMolecular DockingAI Model for Predicting Binding Affinity of Antidiabetic Compounds Targeting PPAR
This study aims to develop a deep learning model for predicting the binding affinity of ligands targeting the Peroxisome Proliferator-Activated Receptor (PPAR) family, using 2D molecular descriptors. A dataset of 3,764 s…
Drug DiscoveryMolecular DockingPLD-Tree: Persistent Laplacian Decision Tree for Protein-Protein Binding Free Energy Prediction
Recent advances in topology-based modeling have accelerated progress in physical modeling and molecular studies, including applications to protein-ligand binding affinity. In this work, we introduce the Persistent Laplac…
Language ModelingLanguage ModellingLarge Language ModelMolecular DockingIn Silico Pharmacokinetic and Molecular Docking Studies of Natural Plants against Essential Protein KRAS for Treatment of Pancreatic Cancer
A kind of pancreatic cancer called Pancreatic Ductal Adenocarcinoma (PDAC) is anticipated to be one of the main causes of mortality during past years. Evidence from several researches supported the concept that the oncog…
Molecular DockingScaling Structure Aware Virtual Screening to Billions of Molecules with SPRINT
Virtual screening of small molecules against protein targets can accelerate drug discovery and development by predicting drug-target interactions (DTIs). However, structure-based methods like molecular docking are too sl…
Drug DiscoveryMolecular DockingGNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking
Molecular docking is a major element in drug discovery and design. It enables the prediction of ligand-protein interactions by simulating the binding of small molecules to proteins. Despite the availability of numerous d…
Blind DockingDrug DiscoveryGraph Neural NetworkMolecular DockingDockformer: A transformer-based molecular docking paradigm for large-scale virtual screening
Molecular docking is a crucial step in drug development, which enables the virtual screening of compound libraries to identify potential ligands that target proteins of interest. However, the computational complexity of …
Drug DesignMolecular DockingQuickBind: A Light-Weight And Interpretable Molecular Docking Model
Predicting a ligand's bound pose to a target protein is a key component of early-stage computational drug discovery. Recent developments in machine learning methods have focused on improving pose quality at the cost of m…
Drug DiscoveryMolecular DockingPose Prediction