Blind Docking

Benchmarks archive 2025-07-28

2 leaderboard tables shown for this task, 2 with rows (a “benchmark” on this site is a table with at least one row, as on /sota), ordered by row count. “Best model” is the first row in the archive's own order at snapshot; nothing is re-ranked here and metric direction is not recorded in the archive. PwC's Trend sparklines are not in the archive, so that column is omitted.

Syntology column: samples harvested from the paper's repositories and executed on synthesized fixtures; “ran” is not a correctness claim and does not order the table. A dash means no Syntology record for that paper, not a recorded non-run. Read from the graph 2026-09-24.

Libraries

Not in the archive: the export carries no per-task library table, so there is nothing to show at snapshot 2025-07-28.

Datasets archive 2025-07-28

No dataset record in the archive lists this task.

Subtasks archive 2025-07-28

No subtask under this task in the archive's task tree.

Parent tasks archive 2025-07-28

Most implemented papers archive 2025-07-28

12 shown of 12 papers with code (19 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• Fast and Accurate Blind Flexible Docking
  20 Feb 2025 2 repositories listed Syntology ran 3 of 4 samples · 1 unverified
  Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery.
• FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction
  14 Dec 2024 2 repositories listed Syntology ran 0 of 10 samples · 10 unverified
  Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation.
• Deep Confident Steps to New Pockets: Strategies for Docking Generalization
  28 Feb 2024 2 repositories listed Syntology ran 3 of 3 samples · 0 unverified
  Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome.
• DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
  4 Oct 2022 2 repositories listed Syntology ran 7 of 12 samples · 5 unverified
  We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses.
• State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
  30 Sep 2022 2 repositories listed
  The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life.
• PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking
  3 May 2025 1 repository listed Syntology ran 0 of 5 samples · 5 unverified
  Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications.
• SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation
  26 Feb 2025 1 repository listed
  Both types of molecules form a ternary complex linking an E3 ligase with a target protein, a crucial step for drug discovery.
• Accurate Pocket Identification for Binding-Site-Agnostic Docking
  4 Feb 2025 1 repository listed
  Accurate identification of druggable pockets is essential for structure-based drug design.
• DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking
  15 Oct 2024 1 repository listed
  Despite these advancements, current methods are often tailored for specific docking settings, and limitations such as the neglect of protein side-chain structures, difficulties in handling large binding pockets, and…
• FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation
  29 Mar 2024 1 repository listed
  Molecular docking is a pivotal process in drug discovery.
• FABind: Fast and Accurate Protein-Ligand Binding
  10 Oct 2023 1 repository listed
  In this work, we propose 𝐅𝐀𝐁𝐢𝐧𝐝, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding.
• EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction
  7 Feb 2022 1 repository listed Syntology ran 0 of 1 samples · 1 unverified
  Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery.

Syntology lines on 6 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced. Read from the graph 2026-09-24.