Blind Docking
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Benchmarks
Most implemented
Fast and Accurate Blind Flexible Docking
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction
Deep Confident Steps to New Pockets: Strategies for Docking Generalization
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking
Papers
Seq2Bind Webserver for Decoding Binding Hotspots directly from Sequences using Fine-Tuned Protein Language Models
Decoding protein-protein interactions (PPIs) at the residue level is crucial for understanding cellular mechanisms and developing targeted therapeutics. We present Seq2Bind Webserver, a computational framework that lever…
Blind DockingPoseX: 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 DockingSE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation
Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable". Proteolysis-targeting chimeras (PROTA…
Blind DockingDecoderDrug DiscoveryGraph Attention+1Fast 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+1Accurate Pocket Identification for Binding-Site-Agnostic Docking
Accurate identification of druggable pockets is essential for structure-based drug design. However, most pocket-identification algorithms prioritize their geometric properties over downstream docking performance. To addr…
Blind DockingDrug DesignGroup 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 Docking